title: C. albicans SN95 prp19Δ/Δ, 39°C YPD, batch2, rep3

city: Berlin

first: Lydia

last: Herzel

address: Takustr. 6

department: Biology, Chemistry and Pharmacy

institute: Freie Universität

data_processing:
Paired-end RNA-seq data were trimmed with cutadapt/2.10 to remove any residual adaptor sequences using the following flags and settings: cutadapt --cores=0 -b CTGTCTCTTATACACATCT -B CTGTCTCTTATACACATCT -e 0.1 -O 10 -m 16 --output=R1t.fastq.gz --paired-output=R2t.fastq.gz $R1 $R2 (Martin, 2011).
Trimmed data were mapped to the Candida albicans SC5314 genome, version A22 with HISAT version 2.2.1 using the following command: hisat2 --summary-file summary.txt --max-intronlen 2000 -x C_albicans_SC5314_A22 --rna-strandness FR -1 $R1 -2 $R2 -S out.sam --novel-splicesite-outfile novelSS.txt (Kim et al., 2015).
Using samtools, bedtools and igvtools (SAMtools/1.16.1, BEDTools/2.30.0, igvtools 2.14.1), hisat2 output was further filtered to retain only mapped reads and converted into bam- and coverage-files (tdf and bedgraph) for visualization in IGV and downstream analyses (Li et al., 2009; Quinlan and Hall, 2010; Thorvaldsdóttir et al., 2013).
Assembly: Candida albicans SC5314 genome, version A22
Supplementary files format and content: TDF File (read coverage)
Supplementary files format and content: Text File (read counts per gene)

organism: Candida albicans

source_name: prp19{delta}/{delta} SN95

growth_protocol: To prepare cell pellets for RNA extraction, saturated overnight cultures grown at 30 °C with shaking in YPD were sub-cultured to an approximate OD600 of 0.1 and grown for 4 hours in the indicated condition, with shaking.

extract_protocol:
Cells were lysed by bead beating, followed by RNA extraction using the RNAeasy kit (Qiagen) and DNase treatment using the DNA-free DNA removal kit (Invitrogen).
Sample libraries were prepared using the Illumina Stranded mRNA Ligation Kit and sequenced with the Illumina Novaseq 6000 using a 100bp paired-end protocol and multiplexing to obtain >25 million paired-end reads/sample.

treatment_protocol: Cells were either grown for 4 hours at 30 °C in YPD, 37 °C and 10% FBS in YPD or 39 °C.

value: prp19{delta}/{delta} SN95

value: 4 hours 39°C with shaking


title: Liver_ST_Adar1wt/wt 2

status: Public on May 28 2024

type: SRA

city: Singapore

first: jinghe

last: xie

address: 21 Lower Kent Ridge Road

country: Singapore

institute: nuh

description: 10X Visium platform

library_source: transcriptomic

data_processing:
space ranger
seurat
R in-house scripts
Library strategy: Spatial transcriptomics sequencing

molecule: polyA RNA

organism: Mus musculus

source_name: Liver

extract_protocol:
Visium spatial gene expression kit (10x Genomics) was used. Briefly, immediately after mice were sacrificed, the livers were removed, cut into appropriately sized pieces, and embedded in OCT using an isopentane bath and liquid nitrogen. OCT sections were collected in a cryostat at 10µm per section. Three sections of each tissue were collected onto mRNA capture slides. Only samples with RIN quality more than 7 were used. Tissues were fixed in -20°C chilled methanol before H&E staining according to manufacturer’s protocol (CG000160 Rev B). Tissue optimization as performed according to manufacturer’s protocol to determine optimal permeabilization conditions (CG000238). Briefly, permeabilization enzyme was applied to H&E-stained tissues on optimization slide and a permeabilization time course was performed before fluorescent cDNA synthesis, tissue removal and slide imaging. All imaging was performed on EVOS M7000 imaging system (Thermo Fisher Scientific).
Tissue permeabilization was performed on Visium gene expression slides to release poly-adenylated mRNA from cells for capture by primers on ST spots underneath, followed by reverse transcription to generate barcoded full length cDNA. cDNA was amplified and cleanup performed using SPRIselect Reagent (Beckman Coulter, B23317). Library preparation was performed according to manufacturer’s protocol to generate libraries containing P5 and P7 Illumina primer sequences, Sample indexes i5 and i7 (10x, 3000431), TruSeq Read 1 and 2 sites, 10x Spatial Barcode, Unique Molecular Identifier (UMI), and inserts (CG000239 Rev D). 9 generated libraries were pooled and sequenced in one lane using Novaseq-6000 S4 for a depth of 2.5B total Paired end reads.

tag: tissue

value: Liver

tag: strain

tag: genotype

value: Ifih1-/- Adar1wt/wt Alb-Cre+

tag: Sex

value: female

tag: age

value: 8 weeks


title: Liver_ST_Adar1flox/flox 1

description: 10X Visium platform

value: Ifih1-/- Adar1flox/flox Alb-Cre+


title: Ctrl.-2 repl.-2

city: Freiburg

first: Manuel

last: Rogg

state: Baden Wuerttemberg

address: Breisacher Straße 115a

department: Institute of Surgical Pathology

country: Germany

institute: University Medical Center Freiburg

description: featureCounts: Counts; sgCtrl.-2 repl.-2

data_processing:
The Galaxy Europe resource was used forprocessing and analysis of sequencing data (https://usegalaxy.eu).
Sequenced reads were quality and adapter trimmed using fastp v0.23.2.
Reads were mapped to hg38 whole genome using HISAT2 v2.2.1 with default settings for paired-end libraries.
featureCounts v2.0.1 and DESeq2 v2.11.40.8 were applied for differential expression analysis
Assembly: Human Dec. 2013 (GRCh38/hg38) (hg38)
Supplementary files format and content: tab-delimited text files include normalized counts for all samples

organism: Homo sapiens

source_name: Control 2

growth_protocol: Cells were cultured in RPMI 1640 cell growth medium supplemented with Glutamine (Thermo Fisher Scientific, #61870036), 10 % FCS (Merck, #S0615) and Penicillin-Streptomycin (Thermo Fisher Scientific, #15140122), 95% air and 5% CO2. Equalized numbers of cell lines were seeded into cell culture dishes and cultured for 24 hours (non-confluent cell culture).

extract_protocol:
Cell were washed in PBS, scraped into PBS and pelleted by centrifugation. RNA was isolated from cell pellets using the Monarch Total RNA Miniprep Kit (T2010S, New England Biolabs) including gDNA depletion by gDNA binding columns and on column DNase-1 digest according to the supplier instructions. RNA quality number (RQN) was measured as >9.3 for all samples using an Agilent Fragment Analyzer system.
After polyA selection, RNA libraries were prepared for sequencing using the NEBnext ultra II RNA kit. Libraries were sequenced on the Illumina NovaSeq 6000 sequencer following the manufacturer's protocols.

tag: cell line_source

tag: cell type

value: kidney cancer

value: wild type control

tag: cell line

value: Control 2

tag: treatment

value: non-targeting sgRNA-2


title: HCC_Non-Tumor_scRNAseq

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Non-tumor and Tumor HCC liver tissues were gently dissociated by mechanical dissection to using forceps and scissors in Collagenase/Dispase (Roche 10269638001) over 2-3 hours at 37°C. Cells were then passed through a 100µm cell strainer and washed with 30ml Advanced DMEM/F12 (Gibco 12634-010) and centrifuged at 100g for 5 mins at 4°C. Red blood cells were lysed by resuspending cell pellet in RBC lysis buffer (Invitrogen 00-4333-57) for 1 minute, diluted with 30ml cold Advanced DMEM/F12 and centrifuged again. Cells were briefly washed cold Advanced DMEM/F12 containing 0.5U/ml RQ1 RNase-free DNaseI (Promega M6101), diluted with 30ml cold Advanced DMEM/F12 and centrifuged again. The live cells were resuspended in cold Advanced DMEM/F12, passed through a 40µm cell strainer to obtain single cell suspensions, and stained with trypan blue cell stain for viability assessment and manual cell counting prior to scRNA sequencing protocol.
10x Genomics Chromium Next GEM Single Cell 3’ kit v3.1 (Dual index) (CG000315 Rev A) was used according to manufacturer's protocol. Briefly, cell suspensions were loaded onto Chromium Next GEM Chip G for Gel-in-emulsion (GEM) generation at concentrations targeting 10,000 cells recovery per sample along with barcoded Single Cell 3’ V3.1 gel beads for poly-adenylated mRNA capture and partitioning oil. Only cell suspensions with more than 70% viability (determined by trypan blue stain) were used. Following GEM generation, partitioned cells were lysed and captured RNA were reverse transcribed to first-strand cDNA. GEMs were then broken and Dynabeads MyONE SILANE (10x, 2000048) were used for cleanup before full-length, barcoded cDNA was PCR amplified for library construction. Library preparation was performed according to manufacturer's protocol (CG000315 Rev A). This involved enzymatic fragmentation and size selection using SPRIselect Reagent (Beckman Coulter, B23317) to yield libraries containing P5 and P7 Illumina primer sequences, Sample indexes i5 and i7 (10x, 3000431), TruSeq Read 1 and 2 sites, 10x Barcode, Unique Molecular Identifier (UMI), and inserts. For human HCC scRNA sequencing experiments, 2 generated libraries were pooled and sequenced in one lane using HiSeq X for 367M total Paired end reads.

tag: disease

value: non-tumor HCC


title: C. albicans SN95 prp19Δ/Δ, 39°C YPD, batch2, rep2


title: Liver_ST_Adar1wt/wt 1

description: 10X Visium platform


title: C. albicans SN95 prp19Δ/Δ, 39°C YPD, batch2, rep1


title: patient 9 healthy-adjacent kidney, emulsion 1, scRNA-seq

city: Vilnius

first: Justina

last: Zvirblyte

state: LT

address: Sauletekio av.7

department: Life Sciences Center, Institute of Biotechnology

country: Lithuania

institute: Vilnius University

description: library name' N9_1 in adata file 'all_cells_50236_33538.h5ad'

data_processing:
The STARsolo pipeline (https://github.com/jsimonas/solo-in-drops) was used to process the data and to obtain expression matrices. STAR (version 2.7.6a) was run with the following parameters: --soloMultiMappers Uniform, -- soloType CB_UMI_Simple, -- soloUMIfiltering MultiGeneUMI, and --soloCBmatchWLtype 1MM.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: healthy-adjacent kidney

extract_protocol:
Patient derived tumor tissues were dissociated using Tumor Dissociation Kit (Miltenyi Biotec, cat.no.130-095-929) in an automated instrument gentleMACS Octo Dissociator with Heaters (Miltenyi Biotec) as per manufacturer’s instructions. Healthy-adjacent tissues were dissociated using Tissue Dissociation Kit I (Miltenyi Biotec, cat.no. 130-110-201). After dissociation, red blood cells were removed from the samples using RBC lysis reagent (Miltenyi Biotec, cat.no.130-094-183). After RBC lysis, cells were washed 3 times in ice-cold 1X DPBS (Gibco, cat.no. 14080-048) at 500g for 5 min. Cell viability and count was assessed using Trypan Blue dye (Gibco, cat.no. 15250061) on a hemocytometer. No further enrichment or selection of cells was performed. Cell suspension was immediately loaded onto inDrops platform for cell barcoding experiment
We isolated the cells at occupancy 0.1 alongside with barcoding beads (Atrandi Biosciences, cat.no. DG-BHB-C) and reverse transcription/lysis mix, the latter supplemented with a template switching oligonucleotide, TSO (see Table 2 for composition). We used cell barcoding chip (Atrandi Biosciences, cat.no. MCN-05) to inject the cells, DNA barcoding beads, and RT/lysis mix at flow rates of 250, 60, 250 µl/hr, respectively. The droplet stabilization oil (Atrandi Biosciences, cat. no. MON-DSO2) was set at 700 µl/hr. The emulsion was collected off-chip on ice rack and briefly exposed to UV light (5 min at 6.5 J/cm2 of 350 nm, Atrandi Biosciences, cat.no. MHT-LAS2) to release the photo-cleavable RT primers from the barcoding hydrogel beads. The RT reaction was performed at 42 °C for 60 min followed by 5 min at 85 °C. The post-RT emulsion was burst with 10% emulsion breaker (Atrandi Biosciences, cat.no. MON-EB1) and pooled material was used for subsequent library construction.The barcoded-cDNA was purified twice with 0.8X AMPure XP reagent (BeckMan Coulter, cat.co. A63881) as per manufacturer’s instructions. Next, cDNA was PCR amplified with KAPA HiFi Hot Start Ready Mix (Roche, cat.no. KK2601) using cDNA FWD primer and cDNA REV primers (see Table 3). Amplified DNA was fragmented and ligated to adapter using instruction and reagents provided by NEBNext® Ultra™ II FS DNA Library Prep (NEB, cat.no. E7805S). Finally, the libraries were amplified by 12-rounds of indexing PCR (2X KAPA HiFi Hot Start Ready Mix, Roche, cat.no. KK2601). Library quality was assessed using Bioanalyzer DNA High Sensitivity chip (Agilent, cat.no. 50674626). The libraries were sequenced on Illumina NextSeq 550 platform in multiple batches using either NextSeq 500/550 High Output Kit v2.5 (75 Cycles) (Illumina, cat.no. 20024906) or NextSeq 500/550 High Output Kit v2.5 (150 Cycles) (Illumina, cat.no. 20024907).

value: healthy-adjacent kidney

value: Female

tag: tumor stage

tag: barcoding bead_version

value: version 2

value: surgery


title: Ctrl.-2 repl.-1

description: featureCounts: Counts; sgCtrl.-2 repl.-1


title: patient 7 healthy-adjacent kidney, emulsion 1, scRNA-seq

description: library name' N7_1 in adata file 'all_cells_50236_33538.h5ad'

value: Male


title: patient 8 healthy-adjacent kidney, emulsion 1, scRNA-seq

description: library name' N8_1 in adata file 'all_cells_50236_33538.h5ad'


title: C. albicans SN95 prp19Δ/Δ, 30°C YPD, batch2, rep2

value: prp19{delta}/{delta} SN95

value: 4 hours 30°C with shaking


title: Ctrl.-1 repl.-2

description: featureCounts: Counts; sgCtrl.-1 repl.-2

source_name: Control 1

value: Control 1

value: non-targeting sgRNA-1


title: C. albicans SN95 prp19Δ/Δ, 30°C YPD, batch2, rep3


title: Ctrl.-1 repl.-1

description: featureCounts: Counts; sgCtrl.-1 repl.-1


title: RNA-nT2

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

country: USA

institute: St Jude Children's Research Hosipital

description: rRNA depleted, stranded RNA

data_processing:
Basecalls performed using CASAVA
Paired-end reads were mapped by STAR(v2.5.2b) using parameters "--outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000  --twopassMode Basic --outFilterScoreMinOverLread 0.33 --outFilterMatchNminOverLread 0.33 " and counted reads by HTSEQ(0.6.1p1) on GENCODE annotation(vM14).
The rRNA depleted samples were processed early using STAR(2.3.0e_r291) with default parameters and also counted by HTSEQ based on GENCODE(vM6).
Genome_build: mm10(GRCm38)
Supplementary_files_format_and_content: gene-based raw counts txt file

molecule: total RNA

source_name: Wild-type naïve T cells

growth_protocol: CD4 naïve T cells from male Foxp3-gfp reporter mice were sorted to induce regulatory T cells in vitro (iTreg) by plate-bound anti-CD3 and anti-CD28 antibodies, recombinant Interleukin-2 (IL-2), TGF-beta, and ascorbic acid. Four days later, cells were starved in IL-2 free medium overnight before being stimulated with IL-2. iTreg cells used for TCR restimulation were not starved.

extract_protocol:
Cells were lysed with the TRIzol reagent and stored at -80C. Total RNA extraction, sequencing library preparation, and deep sequencing were conducted by the Hartwell Center at St. Jude Children’s Research Hospital according to standard protocols.
Libraries were constructed by the Hartwell Center at St. Jude Children’s Research Hospital according to standard protocols for RNA sequencing.

treatment_protocol: After an overnight starvation in IL-2 free medium, iTreg cells were stimulated with mock or 500 U/mL recombinant IL-2 at 37C for 30 min. TCR restimulation was conducted on plates precoated with 1 microgram/mL anti-CD3 and 1 microgram/mL anti-CD28 antibodies in PBS at 37C for 2 hours. Cells were cultured on these plates at 37C for 3 hours before being harvested for RNA extraction and deep sequencing.

tag: gender

value: Wild-type naive T cells

value: Foxp3-gfp mice


title: patient 6 healthy-adjacent kidney, emulsion 1, scRNA-seq

description: library name' N6_1 in adata file 'all_cells_50236_33538.h5ad'


title: RNA-rTreg1

description: rRNA depleted, stranded RNA

source_name: Wild-type regulatory T cells Resting

value: Wild-type regulatory T cells Resting


title: RNA-rTreg2

description: rRNA depleted, stranded RNA


title: C. albicans SN95, 39°C YPD, batch2, rep3

source_name: wild-type SN95

value: wild-type SN95

value: 4 hours 39°C with shaking


title: THP-1 cells,HSV-1,24H,REP1

city: Wuhan

first: Chen-Yu

last: Wang

state: Hubei

address: 299 Bayi Road, Wuchang District

country: China

institute: Wuhan University

data_processing:
The adaptor sequence was removed using Cutadapt (version 1.16) to clean RNA-seq raw data.
Cleaned reads were aligned to the human reference genome (hg19) using HISAT2 (2.1.0) with default settings. Uniquely aligned reads were counted at gene regions using the package feature Counts (version 1.4.6) based on Gencode v19 annotations.
Assembly: hg19
Supplementary files format and content: Tab-delimited execl files include FPKM values for each Sample

growth_protocol: THP-1 cells were maintained in 1640 supplemented with 10% fetal bovine serum(FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted from cells or tissues using TRIzol (Aidlab. biotech)
RNA-seq libraries were constructed with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490) and NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module (NEB E6111). RNA-seq libraries were sequenced by Illumina Nova-seq platform with pair-end reads of 150 bp. Quality control of mRNA-seq data was performed using Fatsqc

treatment_protocol:
The THP-1 cells were infected with HSV-1 (MOI=1) for 24 h.
NR2F6 was knocked down in THP-1 cells with CRISPR and then infected with HSV-1(MOI=1) for 24 h.

value: WT


title: patient 5 healthy-adjacent kidney, emulsion 1, scRNA-seq

description: library name' N5_1 in adata file 'all_cells_50236_33538.h5ad'


title: RNA-nT1

description: rRNA depleted, stranded RNA


title: RNA-aTreg2

description: rRNA depleted, stranded RNA

source_name: Wild-type regulatory T cells Activated

value: Wild-type regulatory T cells Activated


title: patient 4 healthy-adjacent kidney, emulsion 2, scRNA-seq

description: library name' N4_2 in adata file 'all_cells_50236_33538.h5ad'

value: version 1


title: THP-1 cells,Mock,REP2

value: NR2F6 knockdown#1

value: Mock


title: C. albicans SN95 prp19Δ/Δ, 30°C YPD, batch2, rep1


title: RNA-aTreg1

description: rRNA depleted, stranded RNA


title: patient 4 healthy-adjacent kidney, emulsion 1, scRNA-seq

description: library name' N4_1 in adata file 'all_cells_50236_33538.h5ad'

value: healthy-adjacent kidney


title: THP-1 cells,HSV-1,24H,REP2


title: C. albicans SN95, 39°C YPD, batch2, rep2


title: THP-1 cells,Mock,REP1


title: C. albicans SN95, 39°C YPD, batch2, rep1


title: THP-1 cells,NR2F6_KD2,HSV-1,24H

value: NR2F6 knockdown#2


title: patient 3 healthy-adjacent kidney, emulsion 2, scRNA-seq

description: library name' N3_2 in adata file 'all_cells_50236_33538.h5ad'

value: Male

value: surgery


title: RNA-aTe2

description: rRNA depleted, stranded RNA

source_name: Wild-type effector T cells

value: Wild-type effector T cells


title: C. albicans SN95, 30°C YPD, batch2, rep3

value: 4 hours 30°C with shaking


title: RNA-aTe1

description: rRNA depleted, stranded RNA


title: patient 3 healthy-adjacent kidney, emulsion 1, scRNA-seq

description: library name' N3_1 in adata file 'all_cells_50236_33538.h5ad'


title: C. albicans SN95, 30°C YPD, batch2, rep2


title: THP-1 cells,NR2F6_KD2,Mock


title: patient 2 healthy-adjacent kidney, emulsion 2, scRNA-seq

description: library name' N2_2 in adata file 'all_cells_50236_33538.h5ad'


title: C. albicans SN95, 30°C YPD, batch2, rep1


title: THP-1 cells,NR2F6_KD1,HSV-1,24H


title: C. albicans SN95, 39°C YPD, batch1, rep3


title: RNA-1835237_plusTCRa

description: Stranded mRNA

source_name: In vitro induced wild-type regulatory T cells

value: 3 hour stimulation with plate-bound anti-CD3 and anti-CD28 antibodies. Plates were precoated with 1 microgram/mL anti-CD3 and 1 microgram/mL anti-CD28 antibodies in PBS at 37C for 2 hours.


title: patient 1 healthy-adjacent kidney, emulsion 1, scRNA-seq

description: library name' N1_1 in adata file 'all_cells_50236_33538.h5ad'

value: Female


title: RNA-1835236_minusTCRb

description: Stranded mRNA

value: In vitro induced wild-type regulatory T cells

value: Mock treatment of TCR stimulation.

value: Foxp3-gfp mice


title: patient 2 healthy-adjacent kidney, emulsion 1, scRNA-seq

description: library name' N2_1 in adata file 'all_cells_50236_33538.h5ad'


title: C. albicans SN95, 39°C YPD, batch1, rep2

value: wild-type SN95

value: 4 hours 39°C with shaking


title: THP-1 cells,Ctrl,HSV-1,24H

description: THP-1_Ctrl_ HSV-1_24h

value: WT


title: RNA-1835235_minusTCRa

description: Stranded mRNA


title: THP-1 cells,Ctrl,Mock

description: THP-1_Ctrl_ Mock


title: C. albicans SN95, 39°C YPD, batch1, rep1


title: patient 9 tumor, emulsion 2, scRNA-seq

description: library name' T9_2 in adata file 'all_cells_50236_33538.h5ad'

source_name: ccRCC tumor

value: ccRCC tumor

value: version 2


title: THP-1 cells,K27AC,HSV-1,24H,REP2

library_source: genomic

data_processing:
The adaptor sequence was removed using Cutadapt (version 1.16) to clean ChIP-seq raw data.
Cleaned reads were mapped into human reference genome (hg19) using BWA (version 0.7.15) with default settings.
Peak calling for tissues was performed by MACS2 with a p-value threshold of 1E-8. We calculated the normalized FPKM as the ChIP-seq signal in specific region. Then HOMER (http://homer.ucsd.edu/homer/index.html,v4.9,2-20-2017) annotatePeaks.pl was used to annotate ChIP-seq peaks compare to reference genome hg19. HOMER findMotifsGenome.pl was used to find out significant enriched motif.
Assembly: hg19
Supplementary files format and content: bigwig files were generated using deeptools 3.1.3; Scores represent RPKM

molecule: genomic DNA

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 min.After qunenching and cell lysis, chromatin was sonicated.
ChIP-seq libraries were constructed with ChIP and input DNA using VATHS Universal DNA Library Prep Kit for Illumina (Vazyme ND606). Briefly, 50 μL of DNA (8-10 ng) was end-repaired for dA tailing, followed by adaptor ligation. Each adaptor was marked with an 8-bp DNA barcode. Adaptor-ligated DNA was purified by AMPure XP beads (1:1) and then amplified by PCR of 9 cycles with the primer matching with adaptor universal part. Amplified DNA was purified again using AMPure XP beads (1:1) in 35 μL EB elution buffer. For multiplexing, libraries with different barcodes were mixed with equal molar quantities (30-50 million reads per library). Libraries were sequenced by Illumina Nova-seq platform with pair-end reads of 150 bp.

treatment_protocol: THP-1 cells were infected with HSV-1 (MOI=1) for 24 h


title: RNA-1835234_plusIL2b

description: Stranded mRNA

value: 30 min stimulation with 500 U/mL recombinant IL-2.


title: patient 9 tumor, emulsion 1, scRNA-seq

description: library name' T9_1 in adata file 'all_cells_50236_33538.h5ad'


title: RNA-1835233_plusIL2a

description: Stranded mRNA


title: THP-1 cells,K27AC,HSV-1,24H,REP1


title: C. albicans SN95, 37°C YPD + 10% NBCS, batch1, rep2

value: 4 hours 37°C with shaking


title: RNA-1835238_plusTCRb

description: Stranded mRNA


title: patient 8 tumor, emulsion 3, scRNA-seq

description: library name' T8_3 in adata file 'all_cells_50236_33538.h5ad'


title: RNA-1835232_minusIL2b

description: Stranded mRNA

value: Mock treatment for IL-2


title: THP-1 cells,NR2F6_KD1,Mock

value: NR2F6 knockdown#1

value: Mock


title: C. albicans SN95, 37°C YPD + 10% NBCS, batch1, rep1


title: patient 8 tumor, emulsion 2, scRNA-seq

description: library name' T8_2 in adata file 'all_cells_50236_33538.h5ad'

value: surgery


title: THP-1 cells,K27AC,Mock,REP2


title: RNA-1835231_minusIL2a

description: Stranded mRNA

value: Male


title: THP-1 cells,K27AC,Mock,REP1


title: 1436478_Foxp3_PSI_3

description: PSI ChIP

data_processing:
ChIP-seq data analysis: Single reads of 50 bp were mapped mouse genome mm9 (MGSCv37 from Sanger) by BWA (version 0.7.12-r1039, default parameter), duplicated reads were then marked with biobambam2 (version v2.0.87), and non-duplicated reads were chosen by samtools (parameter “-q 1 -F 1024” version 1.2).
We followed ENCODE guideline for quality control of our data. All our samples passed QC criterion and have more than 30M non-duplicated reads.
After assessing the data quality, we extended reads to fragment size (detected by SPP v1.1) and generated bigwig tracks (normalized to 15 million uniquely mapped reads) for visualization. We then called peaks using MACS2(version 2.1.1.20160309, parameters “--nomodel --extsize fragment size”). We confirmed the PSI samples were highly reproducible that > 90% of peaks in one replicate could be called in another.
Genome_build: mm9(MGSCv37 )
Supplementary_files_format_and_content: bigwig

source_name: Male mice

growth_protocol: CD4 naïve T cells from male Foxp3-gfp reporter mice were sorted to induce regulatory T cells in vitro (iTr) by plate-bound anti-CD3 and anti-CD28 antibodies, recombinant Interleukin-2 (IL-2), and TGF-beta, and ascorbic acid-2-phosphate. Four days later, iTr cells were used for Foxp3 PSI or traditional ChIP sequencing.

extract_protocol:
For Foxp3-PSI ChIP, cell fixation and intracellular staining was performed with Foxp3 staining kit (eBioscience). After Foxp3 PSI reaction, cells were fixed with 1% methanol-free formaldehyde at room temperature for 5 min and then sonicated for enrichment of biotinylated chromatins with streptavidin beads. Precipitated DNA was released by proteinase K digestion, phenol: chloroform extraction, and 2-propanol precipitation. Traditional Foxp3 ChIP was conducted according to standard protocols (PMID: 23021222).
Libraries were constructed according to standard protocols for ChIP

treatment_protocol: iTr cells were treated with 0.25 mM ascorbic acid 2-phosphate for 4 days during Treg induction to induce Tet-mediated DNA demethylation naturally occurring during Tr differentiation in vivo.

tag: chip antibody

value: Primary antibody:Rat anti mouse Foxp3 Clone FJK-16s (eBioscience). Secondary antibody:HRP-donkey anti-rat (Thermo Fisher Scientific, A18745).


title: patient 9 tumor, emulsion 3, scRNA-seq

description: library name' T9_3 in adata file 'all_cells_50236_33538.h5ad'

value: Female


title: C. albicans SN95, 30°C YPD, batch1, rep2

value: 4 hours 30°C with shaking


title: THP-1 cells,INPUT,HSV-1,24H,REP2


title: C. albicans SN95, 37°C YPD + 10% NBCS, batch1, rep3


title: 1436477_Foxp3_PSI_2

description: PSI ChIP

value: In vitro induced wild-type regulatory T cells


title: C. albicans SN95, 30°C YPD, batch1, rep1


title: THP-1 cells,INPUT,HSV-1,24H,REP1


title: 1436476_Foxp3_PSI_1

description: PSI ChIP


title: TVM6

city: Los Angeles

first: Joshua

middle: Andrew

last: Kochanowsky

state: California

address: 619 Charles E Young Dr E

department: Microbiology, Immunology and Molecular Genetics

institute: University of California Los Angeles

data_processing:
fastq files were aligned to version 64 of T. vaginalis reference genome (TrichDB-64_TvaginalisG32022_AnnotatedTranscripts.fasta) available on TrichDB using kallisto
Adundance.tsv files resulting from the alignments were summarized to genes using the featureCounts algorithm
Expression data was normalized using the VOOM function in the Limma package in R
Differentially expressed genes (³1.5-fold and £5% false discovery rate) were identified by linear modeling and Bayesian statistics using the Limma package
Assembly: version 64 of T. vaginalis reference genome (TrichDB-64_TvaginalisG32022_AnnotatedTranscripts.fasta)
Supplementary files format and content: tab-delimited text files include log2 counts per million (CPM) values for each Sample ...

organism: Trichomonas vaginalis

source_name: Eukaryotic Protist

growth_protocol: Trichomonas vaginalis strain G3 (5x10^5) were grown over night (18hrs) in complete Diamond's media prior to treatment and subsequent RNA isolation.

extract_protocol:
Direct-zolTM RNA Miniprep Kit (Zymo Research; Cat. #R2071) according to the manufacturer’s instructions
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: 1x106 Trichomonas vaginalis parasites were treated with 50 ugs/mL of TvEVs isolated fromT. vaginalis strain B7RC2 for 6hrs in serum free Diamond's media or mock treated for 6hrs in serum free Diamond's media.

value: Eukaryotic Protist

value: wild-type

value: Mock treated


title: Liver_scRNA_Adar1flox/flox

description:
10x Genomics
Sample 3

data_processing:
cellranger
seurat
Assembly: mm10
Supplementary files format and content: barcodes.tsv (barcode-1 corresponds to  Sample 1, barcode-2 corresponds to  Sample 2, barcode-3 corresponds to  Sample 3), features.tsv, matrix.mtx

extract_protocol:
Liver cell isolation was performed via two-step collagenase perfusion on Ifih1-/- Adar1wt/wt Alb-Cre+, Ifih1-/- Adar1wt/flox Alb-Cre+, and Ifih1-/- Adar1flox/flox Alb-Cre+ mice livers. The inferior vena cava of fresh sacrificed mice was punctured with an 18G perfusion needle, and 30ml 37°C warmed perfusion buffer (1x HBSS) was gently perfused through the liver over the course of 5 minutes until the liver appeared pale. Without disturbing the position of the perfusion needle, 30ml 37°C warmed digestion buffer (Collagenase IV in serum-free DMEM) was then perfused through the liver over the course of 5 minutes until the liver became soft. The liver was then aseptically removed from the mouse into cold DMEM containing 10%FBS. After gross dissection of liver lobes, the lobes were perforated using an 18G needle and dissociated hepatocytes were gently released into the media using a cell scraper. Cells were then passed through a 100µm cell strainer and centrifuged at 50g for 5 mins at 4°C. Red blood cells were lysed by resuspending cell pellet in 3ml Ack Lysing buffer (Gibco A10492-01) for 1 minute, diluted with 30ml cold DMEM containing 10%FBS and centrifuged again. live cells were isolated using 10% Percoll (Sigma P1644) gradient centrifugation at 200g for 15 mins at room temperature. The supernatant was aspirated, and remaining cell pellet were briefly washed with cold DMEM containing 10%FBS and 0.5U/ml RQ1 RNase-free DNaseI (Promega M6101), diluted with 30ml cold DMEM containing 10%FBS and centrifuged again. The live cells were resuspended in cold DMEM containing 10%FBS, passed through a 40µm cell strainer to obtain single cell suspensions, and stained with trypan blue cell stain for viability assessment and manual cell counting prior to scRNA sequencing protocol.
10x Genomics Chromium Next GEM Single Cell 3’ kit v3.1 (Dual index) (CG000315 Rev A) was used according to manufacturer's protocol. Briefly, cell suspensions were loaded onto Chromium Next GEM Chip G for Gel-in-emulsion (GEM) generation at concentrations targeting 10,000 cells recovery per sample along with barcoded Single Cell 3’ V3.1 gel beads for poly-adenylated mRNA capture and partitioning oil. Only cell suspensions with more than 70% viability (determined by trypan blue stain) were used. Following GEM generation, partitioned cells were lysed and captured RNA were reverse transcribed to first-strand cDNA. GEMs were then broken and Dynabeads MyONE SILANE (10x, 2000048) were used for cleanup before full-length, barcoded cDNA was PCR amplified for library construction. Library preparation was performed according to manufacturer's protocol (CG000315 Rev A). This involved enzymatic fragmentation and size selection using SPRIselect Reagent (Beckman Coulter, B23317) to yield libraries containing P5 and P7 Illumina primer sequences, Sample indexes i5 and i7 (10x, 3000431), TruSeq Read 1 and 2 sites, 10x Barcode, Unique Molecular Identifier (UMI), and inserts. For mice liver scRNA sequencing experiments, 3 generated libraries were pooled and sequenced in one lane using HiSeq X for 367M total Paired end reads.

value: Liver

value: Ifih1-/- Adar1flox/flox Alb-Cre+

value: male

value: 9 weeks


title: patient 7 tumor, emulsion 1, scRNA-seq

description: library name' T7_1 in adata file 'all_cells_50236_33538.h5ad'

value: ccRCC tumor

value: version 2


title: TVM5


title: THP-1 cells,INPUT,Mock,REP1

value: WT


title: TVM4


title: Liver_scRNA_Adar1wt/flox

description:
10x Genomics
Sample 2

value: Ifih1-/- Adar1wt/flox Alb-Cre+


title: C. albicans SN95, 30°C YPD, batch1, rep3

value: wild-type SN95


title: DHE_treatment_rep3

city: guangzhou

first: shengqi

last: shen

address: zhongshan road #104

institute: GDPH

data_processing:
Raw data quality control was treated with Fastp (version 0.19.7)
Clean trimmed  seq reads were mapped to GRCH38 by STAR2.7.10b with defualt settings
genes counts were calculated by  RSEMv1.3.1
Assembly: GRCH38
Supplementary files format and content: tab-delimited txt files include raw counts for each sample

extract_protocol:
According to the manufacturer’s instructions, total RNA was extracted from cells or tissues using TRIzol (Life Technologies)
NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA)

value: liver cancer cell

value: DHE;Hypoxia


title: Liver_scRNA_Adar1wt/wt

description:
10x Genomics
Sample 1

value: Ifih1-/- Adar1wt/wt Alb-Cre+


title: patient 8 tumor, emulsion 1, scRNA-seq

description: library name' T8_1 in adata file 'all_cells_50236_33538.h5ad'

value: Female

value: surgery


title: TVM3

value: Eukaryotic Protist


title: patient 7 tumor, emulsion 3, scRNA-seq

description: library name' T7_3 in adata file 'all_cells_50236_33538.h5ad'

value: Male


title: Liver_bulk_Adar1flox/flox_rep3

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using NGS portal
Trimmed sequence reads were mapped to GrCM38/mm10 using NGS portal with default parameter.
Read count extraction and normalization were performed using DEseq2

extract_protocol:
Liver cell isolation was performed via two-step collagenase perfusion on Ifih1-/- Adar1wt/wt Alb-Cre+, Ifih1-/- Adar1wt/flox Alb-Cre+, and Ifih1-/- Adar1flox/flox Alb-Cre+ mice livers. Liver cell isolation was performed via two-step collagenase perfusion on Ifih1-/- Adar1wt/wt Alb-Cre+, Ifih1-/- Adar1wt/flox Alb-Cre+, and Ifih1-/- Adar1flox/flox Alb-Cre+ mice livers. The inferior vena cava of fresh sacrificed mice was punctured with an 18G perfusion needle, and 30ml 37°C warmed perfusion buffer (1x HBSS) was gently perfused through the liver over the course of 5 minutes until the liver appeared pale. Without disturbing the position of the perfusion needle, 30ml 37°C warmed digestion buffer (Collagenase IV in serum-free DMEM) was then perfused through the liver over the course of 5 minutes until the liver became soft. The liver was then aseptically removed from the mouse into cold DMEM containing 10%FBS. After gross dissection of liver lobes, the lobes were perforated using an 18G needle and dissociated hepatocytes were gently released into the media using a cell scraper. Cells were then passed through a 100µm cell strainer and centrifuged at 50g for 5 mins at 4°C. Red blood cells were lysed by resuspending cell pellet in 3ml Ack Lysing buffer (Gibco A10492-01) for 1 minute, diluted with 30ml cold DMEM containing 10%FBS and centrifuged again. live cells were isolated using 10% Percoll (Sigma P1644) gradient centrifugation at 200g for 15 mins at room temperature. Total RNA was extracted from cell pellets using TRIZOL-Chloroform method, following use of Rneasy mini plus kit (Qiagen). 1500ug total RNA (RIN>8) was submitted for library construction (Novogene).
Strand-specific library preparation was preformed by Novogene using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) according to manufacturer's protocol with index codes added. Briefly, ribosome RNA was depleted and fragmentation performed using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-) before second strand cDNA was synthesized using DNA Polymerase I and RNase H with the incorporation of dUTP. Overhangs were converted to blunt ends using exonuclease/polymerase activities before adenylation of 3' ends and ligation of NEBNext adaptor within hairpin loop for hybridization. Size selection of purified library fragments were performed using AMPure XP system (Beckman Coulter, Beverly, USA) to digest second strand with size-selected, adaptor ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Library amplification was performed using Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index Primer. The libraries were then sequenced on the Illumina HiSeq X platform.

value: female

value: 7 weeks


title: TVM2

value: wild-type

value: Mock treated


title: patient 7 tumor, emulsion 2, scRNA-seq

description: library name' T7_2 in adata file 'all_cells_50236_33538.h5ad'


title: DHE_treatment_rep1


title: Liver_bulk_Adar1flox/flox_rep2

value: Liver

value: Ifih1-/- Adar1flox/flox Alb-Cre+

value: male

value: 9 weeks


title: THP-1 cells,INPUT,Mock,REP2

value: WT

value: Mock


title: patient 5 tumor, emulsion 2, scRNA-seq

description: library name' T5_2 in adata file 'all_cells_50236_33538.h5ad'

value: ccRCC tumor

value: version 2


title: TVM1


title: patient 6 tumor, emulsion 3, scRNA-seq

description: library name' T6_3 in adata file 'all_cells_50236_33538.h5ad'


title: DMSO_treatment_rep3

value: liver cancer cell

value: DMSO;Hypoxia


title: TVEV6

value: TvEV (50 ugs/mL) for 6hr


title: patient 5 tumor, emulsion 1, scRNA-seq

description: library name' T5_1 in adata file 'all_cells_50236_33538.h5ad'

value: Female

value: surgery


title: DMSO_treatment_rep2


title: Liver_bulk_Adar1flox/flox_rep1

value: female

value: 11 weeks


title: DMSO_treatment_rep1


title: patient 3 tumor, emulsion 2, scRNA-seq

description: library name' T3_2 in adata file 'all_cells_50236_33538.h5ad'

value: Male

value: version 1


title: Liver_bulk_Adar1wt/flox_rep1

value: Liver

value: Ifih1-/- Adar1wt/flox Alb-Cre+


title: TVEV5

value: Eukaryotic Protist

value: wild-type


title: patient 6 tumor, emulsion 1, scRNA-seq

description: library name' T6_1 in adata file 'all_cells_50236_33538.h5ad'


title: patient 4 tumor, emulsion 1, scRNA-seq

description: library name' T4_2 in adata file 'all_cells_50236_33538.h5ad'


title: patient 6 tumor, emulsion 2, scRNA-seq

description: library name' T6_2 in adata file 'all_cells_50236_33538.h5ad'


title: Liver_bulk_Adar1wt/flox_rep2

value: male

value: 9 weeks


title: TVEV4


title: patient 3 tumor, emulsion 1, scRNA-seq

description: library name' T3_1 in adata file 'all_cells_50236_33538.h5ad'

value: ccRCC tumor


title: DHE_high_treatment

value: DHE;Hypoxia


title: DHE_low_treatment

value: liver cancer cell


title: DHE_treatment_rep2


title: TVEV3


title: Liver_bulk_Adar1wt/wt_rep2

value: Ifih1-/- Adar1wt/wt Alb-Cre+


title: TVEV1

value: TvEV (50 ugs/mL) for 6hr


title: Liver_bulk_Adar1wt/wt_rep1


title: patient 2 tumor, emulsion 1, scRNA-seq

description: library name' T2_1 in adata file 'all_cells_50236_33538.h5ad'


title: TVEV2


title: patient 2 tumor, emulsion 2, scRNA-seq

description: library name' T2_2 in adata file 'all_cells_50236_33538.h5ad'


title: ATAC_cDC1_KO_2

status: Public on May 27 2024

city: Vienna

first: Cristiano

last: de Sá Fernandes

address: Borschkegasse 8a

department: Center of Cancer Research

country: Austria

institute: MedicalUniversity of Vienna

data_processing:
Reads alignment was performed using Bowtie2 to the GRCm38(mm10) using the “—very-sensitive” parameter.
Aligned BAM files were then sorted and filtered using ENCODE blacklisted regions and indexed using samtools. For peak calling, MACS2 was used using the “—nomodel”, “—keep-dup auto” and “extsize 147” option for each sample.
Quality metrics were reported using MultiQC 75 and no samples needed to be removed.
Assembly: GRCm38(mm10)
Supplementary files format and content: bigWig files allow visualizattion of aligned data in IGV.
Supplementary files format and content: _summits.bed files contain peak information.

source_name: Spleen

extract_protocol:
spleens were isolated and digested for 15 and 30 minutes respectively, in the presence of Liberase (50µg/ml, Sigma-Aldrich) and DNAse (250µg/ml, Sigma-Aldrich) in PBS supplemented with 5% FCS (Sigma-aldrich). Organs were then mashed through a 70µm filter and spleens were treated with ACK lysis buffer(BioLegend) for red blood cell elimination. Prepared cell suspensions were then pre-enriched using EasyStep pan-DC enrichment kit II (STEM cell) and later stained with FACS antibodies: cDC1 (Lin-CD11c+MHCII+CD64-XCR1+CD11b-), cDC2 (Lin-CD11c+MHCII+CD64-XCR1-CD11b+). Cells were FACS sorted and immediatelly processed for the transposase reaction using the Illumina Tagment DNA TDE1 Enzyme and Buffer kit. Tagmentation reaction was performed at 37ºC, for 30 minutes with 1000rpm incubation. DNA was the isolated using PCR purification kit (Qiagen).
Nextera XT DNA Library Preparation Kit following user guide.

value: Spleen

value: conventional Dendritic Cell 1

value: HDAC1 Mx1-Cre

value: Mice were treated with PolyI/C to induce gene recombination, and cells sorted 2 weeks after.


title: Hi-C of HeLa-S3 UV-exposed, 30mins post-UV

city: Istanbul

first: Ogun

last: Adebali

address: Orta Mahalle, Üniversite Caddesi No:27 Tuzla, Sabancı Üniversitesi

department: Mol. Bio. Genetics & Bioeng.

country: Turkey

institute: Sabanci University

data_processing:
fastq files were first preprocessed to QC with fastp with flag --detect_adapter_for_pe.
Hi-C contacts matrices were generated (.hic format) with the Juicer v1.6 pipeline, with default parameters.
.hic format (q30 filtered) has been converted to .mcool format with hicConvertFormat subprogram of HiCExplorer.
Matrix balancing has been performed with balance subprogram of cooler with parameters --cis-only --max-iters 1000 --blacklist, with ENCODE hg38 blacklisted regions.
Assembly: GRCh38, Gencode v35
Supplementary files format and content: mcool format contains multi-resolution contact matrices in cooler format

source_name: cervix

growth_protocol: HeLa-S3 cells were maintained in Dulbeco’s modified Eagle’s medium (PAN-P04-03500) supplemented with 10% (v/v) heat-inactivated fetal bovine serum (PAN-P30-3304), 100 U/ml penicillin/streptomycin (PAN-P06-07100), 2 mM L-glutamine (PAN-P04-80100) and 1x MEM non-essential amino acid (Gibco 11140-35) solution. Cells were maintained at 37 °C with 5% CO2.

extract_protocol:
Cells were cross-linked with formaldehyde prior to library construction.
The Hi-C library was generated using Phase Genomics Proximo Human Kit version 4.0.

treatment_protocol: With the cover off, cells were placed under a germicidal lamp emitting 254-nm UV (1 J/m2/s) for 20 s.

value: cervix

value: cancer

value: UV


title: ATAC_cDC2 WT_1

value: conventional Dendritic Cell 2

value: HDAC1 floxed


title: Post-UV 12mins RNA-Seq Rep3

data_processing:
fastq files were first preprocessed to QC with fastp with flag --detect_adapter_for_pe.
Reads have been aligned to human genome and its corresponding annotation file, with STAR aligner version 2.7.6a with arguments --genomeLoad NoSharedMemory --quantMode TranscriptomeSAM --twopassMode Basic --outSAMtype BAM SortedByCoordinate
Transcripts (transcripts per million) were quantified using Salmon version 1.6.0
Assembly: GRCh38, Gencode v35
Supplementary files format and content: Salmon output files, contain TPM values for each transcript

extract_protocol:
RNA isolation was carried out using Genezol RNA isolation reagent (Geneaid GZR100) following the manufacturer’s instructions.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.


title: ATAC_cDC2 KO_2


title: Non-UV RNA-Seq Rep3


title: ATAC_cDC2 KO_1


title: Hi-C of HeLa-S3 UV-exposed, 12mins post-UV


title: ATAC_cDC1_KO_1


title: ATAC_cDC1_WT_1


title: Post-UV 60mins RNA-Seq Rep3


title: Hi-C of HeLa-S3 UV-exposed, 60mins post-UV


title: DMSO_treatment

value: DMSO;Hypoxia


title: Hi-C of HeLa-S3


title: ATAC_cDC1_WT_2


title: ATAC_cDC2 WT_2


title: Post-UV 30mins RNA-Seq Rep2


title: Post-UV 12mins RNA-Seq Rep2


title: Non-UV RNA-Seq Rep2


title: Post-UV 30mins RNA-Seq Rep1


title: Post-UV 60mins RNA-Seq Rep1


title: Non-UV RNA-Seq Rep1


title: Post-UV 30mins RNA-Seq Rep3


title: C2

city: Baltimore

first: Dimitrios

last: Avramopoulos

state: Maryland

address: 733 North Broadway

department: Genetic Medicine

institute: Johns Hopkins University

data_processing:
Hisat2 (version 2.2.1)
SAMtools (version 1.1.4)
stringtie (version 2.1.7)
Bioconductor package DESeq2
Assembly: hg38
Supplementary files format and content: csv format, gene expression levels (normalized reaad counts from the DEseq2 package) for each sample

source_name: hiPSC derived excitatory neurons

growth_protocol: Neural maturation medium (Neurobasal medium A (Gibco, Grand Island, NY, USA),

extract_protocol:
Quick-RNA MiniPrep Kit (Zymo Research #R1054)
e 250~300 bp insert , strand-specific libraries with rRNA removal.
Fragmentation, Reverse Transcription, Second strand cDNA synthesis, End repair and A-tailing, , adapter ligation, Size selection, PCR amplification

value: hiPSC derived excitatory neurons

value: not edited


title: D12

value: edited


title: C10


title: C7


title: D4


title: D3


title: C1


title: D10


title: C8


title: A8_4


title: C9


title: Post-UV 60mins RNA-Seq Rep2


title: Vaginal fibroblasts, Lv-CSRNP1-3

city: Shenyang

first: Zhijun

last: Xia

address: 36 Sanhao Street

institute: Shengjing Hospital of China Medical University

description: Vaginal fibroblasts, Lv-CSRNP1, 48 h

data_processing:
Discard a paired reads if either one read contains adapter contamination;
Discard a paired reads if more than 10% of bases are uncertain in either one read;
Discard a paired reads if the proportion of low quality (Phred quality <5) bases is over 50% in either one read.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Vaginal fibroblasts

growth_protocol: Vaginal fibroblasts were maintained in DMEM containing 10% fetal bovine serum and 1% penicillin/streptomycin (P/S) in a humidified incubator with 5% CO2 at 37 °C.

extract_protocol:
Total RNA was extracted from human vaginal fibroblasts with TRIzol (Invitrogen).
Sequencing  libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L) following manufacturer’s recommendations.

treatment_protocol: The vaginal fibroblasts were infected with CSRNP1 overexpressing lentivirus or its control lentivirus (MOI=20) and incubated in a humidified incubator with 5% CO2 at 37 °C for 48 h.

value: Vaginal fibroblasts

value: Fibroblasts


title: Vaginal fibroblasts, Lv-CSRNP1-4

description: Vaginal fibroblasts, Lv-CSRNP1, 48 h


title: Vaginal fibroblasts, Lv-Vector-3

description: Vaginal fibroblasts, Lv-Vector, 48 h

value: Lv-Vector


title: Vaginal fibroblasts, Lv-Vector-4

description: Vaginal fibroblasts, Lv-Vector, 48 h


title: Vaginal fibroblasts, Lv-CSRNP1-2

description: Vaginal fibroblasts, Lv-CSRNP1, 48 h


title: Vaginal fibroblasts, Lv-CSRNP1-1

description: Vaginal fibroblasts, Lv-CSRNP1, 48 h


title: Post-UV 12mins RNA-Seq Rep1


title: Vaginal fibroblasts, Lv-Vector-2

description: Vaginal fibroblasts, Lv-Vector, 48 h


title: Vaginal fibroblasts, Lv-Vector-1

description: Vaginal fibroblasts, Lv-Vector, 48 h


title: KG1a_VEN-2

city: Duarte

first: Hsun

middle: Teresa

last: Ku

state: CA

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

data_processing:
RNA-Seq reads were trimmed to remove sequencing adapters using Trimmomatic and polyA tails using FASTP.
The processed reads were mapped to the human genome hg38 using STAR (v. 2.6.0.a), and gene expression levels were summarized by HTSeq-count v.0.11.1.
Gene expression raw counts were normalized using TMM normalization method and differential expression analysis was conducted using log likelihood ratio test implemented in “edgeR”.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: KG1a cells were cultured in IMDM with 10% FBS, 1% anti-anti.

extract_protocol:
miRNeasy RNA isolation kit (Qiagen)
The libraries were prepared with SMART-Seq® Ultra Low Input RNA Kit for Sequencing – v4 (TaKaRa, Cat. 634888) according to the manufacturer's protocol. The final libraries were validated with the Agilent Bioanalyzer DNA High Sensitivity Kit and quantified with Qubit. Sequencing was performed on Illumina HiSeq 2500 with the single read mode of 51cycle.

treatment_protocol: KG1a cells were treated with TAK-981(5µM), VEN(1µM), or both for 48h. DMSO was used as vehicle control (ctrl).

value: acute myeloid leukemia

value: venetoclax


title: KG1a_T-Plus-V-1

value: TAK-981 + venetoclax


title: KG1a_T-Plus-V-2


title: KG1a_TAK-2


title: KG1a_VEN-1


title: B11_6


title: KG1a_TAK-1


title: KG1a_ctrl-2

value: vehicle control


title: KG1a_ctrl-1


title: CART_ADT_DC61_DC65_DC66_DC67_Duplicate2

city: New Haven

first: Rong

last: Fan

state: Connecticut

address: 55 Prospect St.

department: Biomedical Engineering

institute: Yale University

description:
Reads cover antibody-derived tag (ADT) expression of 17 surface proteins and Hashtag antibodies #1-8
CART_ADT_16

data_processing:
The sequencing data underwent alignment to the GRCh38 human reference genome, followed by barcode and unique molecular identifier counting, ultimately generating a digital gene expression matrix using Cell Ranger v6.1.2 (10x Genomics).
Assembly: GRCh38
Supplementary files format and content: Integrated Seurat .rds object
Library strategy: CITE-seq

source_name: PBMCs

growth_protocol: CAR T cells were thawed, stimulated with CD19-expressing 3T3 cells, and subsequently underwent magnetic selection to isolate the CAR-positive fraction.awed, stimulated with CD19 expressed 3T3 cells, followed by magnetical CAR+ fraction selection.

extract_protocol:
We utilized hashtag reagents for sample barcoding, enabling the amalgamation of eight samples into a single lane for subsequent demultiplexing during analysis. The combined cells were then subjected to incubation in an antibody cocktail comprising 17 TotalSeq™-B anti-human antibodies targeting surface markers. The scRNA-seq libraries were prepared using the Chromium Single-Cell 3’ Library and Gel Bead Kit v3.1 (10x Genomics, Cat# PN-1000268).
Libraries were constructed according to the protocols provided by the 10x Genomics kit.

value: PBMCs

value: Manufactured CAR T cells

tag: library type

value: ADT


title: CART_ADT_DC57_DC58_DC59_DC60_Duplicate2

description:
Reads cover antibody-derived tag (ADT) expression of 17 surface proteins and Hashtag antibodies #1-8
CART_ADT_14


title: CART_ADT_DC61_DC65_DC66_DC67_Duplicate1

description:
Reads cover antibody-derived tag (ADT) expression of 17 surface proteins and Hashtag antibodies #1-8
CART_ADT_15


title: CART_ADT_DC75_DC77_ND365_ND534_Duplicate1

description:
Reads cover antibody-derived tag (ADT) expression of 17 surface proteins and Hashtag antibodies #1-8
CART_ADT_17


title: CART_ADT_DC75_DC77_ND365_ND534_Duplicate2

description:
Reads cover antibody-derived tag (ADT) expression of 17 surface proteins and Hashtag antibodies #1-8
CART_ADT_18


title: CART_ADT_VC38_VC39_DC40_DC41_Duplicate2

description:
Reads cover antibody-derived tag (ADT) expression of 17 surface proteins and Hashtag antibodies #1-8
CART_ADT_10


title: CART_ADT_VC30_VC31_DC32_VC33_Duplicate2

description:
Reads cover antibody-derived tag (ADT) expression of 17 surface proteins and Hashtag antibodies #1-8
CART_ADT_6


title: CART_ADT_DC57_DC58_DC59_DC60_Duplicate1

description:
Reads cover antibody-derived tag (ADT) expression of 17 surface proteins and Hashtag antibodies #1-8
CART_ADT_13


title: CART_ADT_VC38_VC39_DC40_DC41_Duplicate1

description:
Reads cover antibody-derived tag (ADT) expression of 17 surface proteins and Hashtag antibodies #1-8
CART_ADT_9


title: CART_ADT_VC30_VC31_DC32_VC33_Duplicate1

description:
Reads cover antibody-derived tag (ADT) expression of 17 surface proteins and Hashtag antibodies #1-8
CART_ADT_5


title: CART_ADT_VC26_VC27_DC28_VC29_Duplicate2

description:
Reads cover antibody-derived tag (ADT) expression of 17 surface proteins and Hashtag antibodies #1-8
CART_ADT_4


title: CART_ADT_VC34_VC35_DC36_VC37_Duplicate2

description:
Reads cover antibody-derived tag (ADT) expression of 17 surface proteins and Hashtag antibodies #1-8
CART_ADT_8


title: CART_ADT_VC34_VC35_DC36_VC37_Duplicate1

description:
Reads cover antibody-derived tag (ADT) expression of 17 surface proteins and Hashtag antibodies #1-8
CART_ADT_7


title: CART_ADT_VC26_VC27_DC28_VC29_Duplicate1

description:
Reads cover antibody-derived tag (ADT) expression of 17 surface proteins and Hashtag antibodies #1-8
CART_ADT_3


title: CART_ADT_VC22_VC23_DC24_VC25_Duplicate2

description:
Reads cover antibody-derived tag (ADT) expression of 17 surface proteins and Hashtag antibodies #1-8
CART_ADT_2


title: CART_ADT_VC22_VC23_DC24_VC25_Duplicate1

description:
Reads cover antibody-derived tag (ADT) expression of 17 surface proteins and Hashtag antibodies #1-8
CART_ADT_1


title: CART_ADT_VC13_VC14_DC15_VC17_Duplicate1

description:
Reads cover antibody-derived tag (ADT) expression of 17 surface proteins and Hashtag antibodies #1-8
CART_ADT_W


title: CART_ADT_VC18_VC19_DC20_VC21_Duplicate2

description:
Reads cover antibody-derived tag (ADT) expression of 17 surface proteins and Hashtag antibodies #1-8
CART_ADT_Z


title: CART_ADT_VC13_VC14_DC15_VC17_Duplicate2

description:
Reads cover antibody-derived tag (ADT) expression of 17 surface proteins and Hashtag antibodies #1-8
CART_ADT_X


title: CART_ADT_VC18_VC19_DC20_VC21_Duplicate1

description:
Reads cover antibody-derived tag (ADT) expression of 17 surface proteins and Hashtag antibodies #1-8
CART_ADT_Y


title: CART_ADT_VC09_VC10_DC11_VC12_Duplicate1

description:
Reads cover antibody-derived tag (ADT) expression of 17 surface proteins and Hashtag antibodies #1-8
CART_ADT_U


title: CART_ADT_DC49_DC53_DC54_DC56_Duplicate1

description:
Reads cover antibody-derived tag (ADT) expression of 17 surface proteins and Hashtag antibodies #1-8
CART_ADT_11


title: CART_ADT_VC05_VC06_DC07_VC08_Duplicate2

description:
Reads cover antibody-derived tag (ADT) expression of 17 surface proteins and Hashtag antibodies #1-8
CART_ADT_T


title: CART_ADT_VC01_VC03_DC04_VC16_Duplicate2

description:
Reads cover antibody-derived tag (ADT) expression of 17 surface proteins and Hashtag antibodies #1-8
CART_ADT_R


title: CART_ADT_VC09_VC10_DC11_VC12_Duplicate2

description:
Reads cover antibody-derived tag (ADT) expression of 17 surface proteins and Hashtag antibodies #1-8
CART_ADT_V


title: CART_ADT_DC49_DC53_DC54_DC56_Duplicate2

description:
Reads cover antibody-derived tag (ADT) expression of 17 surface proteins and Hashtag antibodies #1-8
CART_ADT_12


title: CART_ADT_DC51_DC68_DC80_VC02_Duplicate1

description:
Reads cover antibody-derived tag (ADT) expression of 17 surface proteins and Hashtag antibodies #1-8
CART_ADT_O


title: CART_ADT_DC51_DC68_DC80_VC02_Duplicate2

description:
Reads cover antibody-derived tag (ADT) expression of 17 surface proteins and Hashtag antibodies #1-8
CART_ADT_P


title: CART_ADT_DC43_DC45_DC76_DC79_Duplicate2

description:
Reads cover antibody-derived tag (ADT) expression of 17 surface proteins and Hashtag antibodies #1-8
CART_ADT_N


title: CART_ADT_VC01_VC03_DC04_VC16_Duplicate1

description:
Reads cover antibody-derived tag (ADT) expression of 17 surface proteins and Hashtag antibodies #1-8
CART_ADT_Q


title: CART_ADT_DC43_DC45_DC76_DC79_Duplicate1

description:
Reads cover antibody-derived tag (ADT) expression of 17 surface proteins and Hashtag antibodies #1-8
CART_ADT_M


title: CART_ADT_DC46_DC55_DC69_DC70_Duplicate2

description:
Reads cover antibody-derived tag (ADT) expression of 17 surface proteins and Hashtag antibodies #1-8
CART_ADT_L


title: CART_ADT_DC42_DC44_DC63_DC82_Duplicate2

description:
Reads cover antibody-derived tag (ADT) expression of 17 surface proteins and Hashtag antibodies #1-8
CART_ADT_J


title: CART_ADT_DC42_DC44_DC63_DC82_Duplicate1

description:
Reads cover antibody-derived tag (ADT) expression of 17 surface proteins and Hashtag antibodies #1-8
CART_ADT_I


title: CART_ADT_DC46_DC55_DC69_DC70_Duplicate1

description:
Reads cover antibody-derived tag (ADT) expression of 17 surface proteins and Hashtag antibodies #1-8
CART_ADT_K


title: CART_ADT_DC50_DC62_DC64_DC73_Duplicate2

description:
Reads cover antibody-derived tag (ADT) expression of 17 surface proteins and Hashtag antibodies #1-8
CART_ADT_H


title: CART_ADT_DC50_DC62_DC64_DC73_Duplicate1

description:
Reads cover antibody-derived tag (ADT) expression of 17 surface proteins and Hashtag antibodies #1-8
CART_ADT_G


title: CART_ADT_DC47_DC72_DC74_DC81_Duplicate1

description:
Reads cover antibody-derived tag (ADT) expression of 17 surface proteins and Hashtag antibodies #1-8
CART_ADT_E


title: CART_ADT_DC47_DC72_DC74_DC81_Duplicate2

description:
Reads cover antibody-derived tag (ADT) expression of 17 surface proteins and Hashtag antibodies #1-8
CART_ADT_F


title: CART_ADT_DC48_DC52_DC71_DC78_Duplicate2

description:
Reads cover antibody-derived tag (ADT) expression of 17 surface proteins and Hashtag antibodies #1-8
CART_ADT_D


title: CART_ADT_DC48_DC52_DC71_DC78_Duplicate1

description:
Reads cover antibody-derived tag (ADT) expression of 17 surface proteins and Hashtag antibodies #1-8
CART_ADT_C


title: CART_ADT_ND585_ND463_ND502_ND317_Duplicate2

description:
Reads cover antibody-derived tag (ADT) expression of 17 surface proteins and Hashtag antibodies #1-8
CART_ADT_B


title: CART_ADT_VC05_VC06_DC07_VC08_Duplicate1

description:
Reads cover antibody-derived tag (ADT) expression of 17 surface proteins and Hashtag antibodies #1-8
CART_ADT_S


title: CART_RNA_DC61_DC65_DC66_DC67_Duplicate1

description:
Hashtag1 for DC61_CD19, Hashtag2 for DC65_CD19, Hashtag3 for DC66_CD19, Hashtag4 for DC67_CD19, Hashtag5 for DC61_Basal, Hashtag6 for DC65_Basal, Hashtag7 for DC66_Basal, Hashtag8 for DC67_Basal
CART_RNA_15

data_processing:
The sequencing data underwent alignment to the GRCh38 human reference genome, followed by barcode and unique molecular identifier counting, ultimately generating a digital gene expression matrix using Cell Ranger v6.1.2 (10x Genomics).
Assembly: GRCh38
Supplementary files format and content: Integrated Seurat .rds object

value: GEX


title: CART_RNA_DC75_DC77_ND365_ND534_Duplicate1

description:
Hashtag1 for DC75_CD19, Hashtag2 for DC77_CD19, Hashtag3 for ND365_CD19, Hashtag4 for ND534_CD19, Hashtag5 for DC75_Basal, Hashtag6 for DC77_Basal, Hashtag7 for ND365_Basal, Hashtag8 for ND534_Basal
CART_RNA_17


title: CART_RNA_DC57_DC58_DC59_DC60_Duplicate1

description:
Hashtag1 for DC57_CD19, Hashtag2 for DC58_CD19, Hashtag3 for DC59_CD19, Hashtag4 for DC60_CD19, Hashtag5 for DC57_Basal, Hashtag6 for DC58_Basal, Hashtag7 for DC59_Basal, Hashtag8 for DC60_Basal
CART_RNA_13


title: CART_ADT_ND585_ND463_ND502_ND317_Duplicate1

description:
Reads cover antibody-derived tag (ADT) expression of 17 surface proteins and Hashtag antibodies #1-8
CART_ADT_A


title: E13.5 Motor neurons, ATAC, NFIA conditional knockout1

city: La Jolla

first: Stacey

middle: Marie

last: Glasgow

address: 9500 Gilman Dr, 3216 Pacific Hall

institute: University of California San Diego

data_processing:
Paired-end FASTQ reads for each replicate were aligned using Bowtie 2.0 (bowtie2 –very-sensitive -k 30) to the mouse genome (mm10).
ATAC-seq data was processed as described in Meharena et al., 2022
ATAC-seq regions were split into peaks occurring within promoters and the GimmeMotifs function (Heeringen 2011) was used with the Homer (Heinz 2010) motif-finding algorithm.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: Spinal cord

extract_protocol:
Spinal cords were harvested from control and NFIAcKO E13.5 embryos carrying the Hb9::GFP transgene. Cells from each spinal cord were dissociated and sorted using a BD FACS Aria II Cell Sorter (UCSD Human Embryonic Stem Cell Core Facility), for GFP+ cells. Freshly-sorted cells were resuspended in cryopreservation solution and frozen at -80oC.
Cells were incubated in permealization buffer (sigma) and centrifuge to obtain pemeabilized nuclei. 50,000 nuclei were tagmented and  purified using MinElute PCR purification kit (Qiagen). Libraries were amplified using NEB Next High-Fidelity 2X PCR Master Mix (NEB) and purified using MinElute PCR purification kit  (Qiagen). Two size selection steps were performed using SPRIselect bead (Beckman Coulter) at 0.55X and 1.5X bead-to-sample volume ratios, respectively. QC data processing was performed as described in Smith et al. 2021.

value: Spinal cord

tag: developmental stage

value: NFIA-ff;Nestin-cre; Hb9::GFP

value: untreated


title: CART_RNA_DC75_DC77_ND365_ND534_Duplicate2

description:
Hashtag1 for DC75_CD19, Hashtag2 for DC77_CD19, Hashtag3 for ND365_CD19, Hashtag4 for ND534_CD19, Hashtag5 for DC75_Basal, Hashtag6 for DC77_Basal, Hashtag7 for ND365_Basal, Hashtag8 for ND534_Basal
CART_RNA_18


title: E13.5 Motor neurons, ATAC, Control2

value: NFIA-ff; Hb9::GFP


title: CART_RNA_VC38_VC39_DC40_DC41_Duplicate1

description:
Hashtag1 for VC38_CD19, Hashtag2 for VC39_CD19, Hashtag3 for VC40_CD19, Hashtag4 for VC41_CD19, Hashtag5 for VC38_Basal, Hashtag6 for VC39_Basal, Hashtag7 for VC40_Basal, Hashtag8 for VC41_Basal
CART_RNA_9


title: CART_RNA_DC49_DC53_DC54_DC56_Duplicate2

description:
Hashtag1 for DC49_CD19, Hashtag2 for DC53_CD19, Hashtag3 for DC54_CD19, Hashtag4 for DC56_CD19, Hashtag5 for DC49_Basal, Hashtag6 for DC53_Basal, Hashtag7 for DC54_Basal, Hashtag8 for DC56_Basal
CART_RNA_12


title: CART_RNA_DC57_DC58_DC59_DC60_Duplicate2

description:
Hashtag1 for DC57_CD19, Hashtag2 for DC58_CD19, Hashtag3 for DC59_CD19, Hashtag4 for DC60_CD19, Hashtag5 for DC57_Basal, Hashtag6 for DC58_Basal, Hashtag7 for DC59_Basal, Hashtag8 for DC60_Basal
CART_RNA_14


title: CART_RNA_VC30_VC31_DC32_VC33_Duplicate1

description:
Hashtag1 for VC30_CD19, Hashtag2 for VC31_CD19, Hashtag3 for VC32_CD19, Hashtag4 for VC33_CD19, Hashtag5 for VC30_Basal, Hashtag6 for VC31_Basal, Hashtag7 for VC32_Basal, Hashtag8 for VC33_Basal
CART_RNA_5


title: Uterus, Control, 4

city: Grand Rapids

first: Genna

middle: E

last: Moldovan

state: MI

address: 400 Monroe Ave NW

department: Obstetrics, Gynecology and Reproductive Biology

institute: Michigan State University

data_processing:
Reads were quality trimmed, adapters were removed using TrimGalore (version 0.6.10), and quality-trimmed reads were assessed with MultiQC (version 1.7).
Trimmed reads were mapped to Mus Musculus GRCm39.110 and gene counts quantified using STAR (version 2.6.0c).
Differential gene expression was performed utilizing edgeR robust
Assembly: GRCm39.110
Supplementary files format and content: tab delimited .txt files containing raw counts

source_name: Pregnant uterus

extract_protocol:
Total RNA was isolated from uteri utilizing TriZol/Phenol red followed by treatment with an RNA Clean and Concentrator Kit from Zymo and DNAse treatment from Invitrogen then eluted in nuclease-free water and sotred at -80C.
Libraries were prepared with Illumina Stranded mRNA Library prep kit.

treatment_protocol: Uterine cross sections were stored in RNAlater solution at -80C prior to isolation.

value: Pregnant uterus

tag: time

value: 7.5 days post coitus

value: Pgr +/+ Yap f/f Wwtr1 f/f


title: CART_RNA_DC49_DC53_DC54_DC56_Duplicate1

description:
Hashtag1 for DC49_CD19, Hashtag2 for DC53_CD19, Hashtag3 for DC54_CD19, Hashtag4 for DC56_CD19, Hashtag5 for DC49_Basal, Hashtag6 for DC53_Basal, Hashtag7 for DC54_Basal, Hashtag8 for DC56_Basal
CART_RNA_11

tag: tissue


title: Uterus, Knockout, 2

value: Pgr Cre/+ Yap +/f Wwtr1 f/f


title: E13.5 Motor neurons, ATAC, NFIA conditional knockout2

tag: strain


title: CART_RNA_VC38_VC39_DC40_DC41_Duplicate2

description:
Hashtag1 for VC38_CD19, Hashtag2 for VC39_CD19, Hashtag3 for VC40_CD19, Hashtag4 for VC41_CD19, Hashtag5 for VC38_Basal, Hashtag6 for VC39_Basal, Hashtag7 for VC40_Basal, Hashtag8 for VC41_Basal
CART_RNA_10


title: CART_RNA_VC34_VC35_DC36_VC37_Duplicate2

description:
Hashtag1 for VC34_CD19, Hashtag2 for VC35_CD19, Hashtag3 for VC36_CD19, Hashtag4 for VC37_CD19, Hashtag5 for VC34_Basal, Hashtag6 for VC35_Basal, Hashtag7 for VC36_Basal, Hashtag8 for VC37_Basal
CART_RNA_8


title: CART_RNA_VC22_VC23_DC24_VC25_Duplicate1

description:
Hashtag1 for VC22_CD19, Hashtag2 for VC23_CD19, Hashtag3 for VC24_CD19, Hashtag4 for VC25_CD19, Hashtag5 for VC22_Basal, Hashtag6 for VC23_Basal, Hashtag7 for VC24_Basal, Hashtag8 for VC25_Basal
CART_RNA_1


title: E13.5 Motor neurons, ATAC, Control1

tag: genotype


title: CART_RNA_VC18_VC19_DC20_VC21_Duplicate1

description:
Hashtag1 for VC18_CD19, Hashtag2 for VC19_CD19, Hashtag3 for VC20_CD19, Hashtag4 for VC21_CD19, Hashtag5 for VC18_Basal, Hashtag6 for VC19_Basal, Hashtag7 for VC20_Basal, Hashtag8 for VC21_Basal
CART_RNA_Y


title: CART_RNA_VC13_VC14_DC15_VC17_Duplicate2

description:
Hashtag1 for VC13_CD19,  Hashtag3 for VC15_CD19, Hashtag4 for VC17_CD19, Hashtag5 for VC13_Basal, Hashtag6 for VC14_Basal, Hashtag7 for VC15_Basal, Hashtag8 for VC17_Basal
CART_RNA_X


title: CART_RNA_VC34_VC35_DC36_VC37_Duplicate1

description:
Hashtag1 for VC34_CD19, Hashtag2 for VC35_CD19, Hashtag3 for VC36_CD19, Hashtag4 for VC37_CD19, Hashtag5 for VC34_Basal, Hashtag6 for VC35_Basal, Hashtag7 for VC36_Basal, Hashtag8 for VC37_Basal
CART_RNA_7


title: CART_RNA_VC30_VC31_DC32_VC33_Duplicate2

description:
Hashtag1 for VC30_CD19, Hashtag2 for VC31_CD19, Hashtag3 for VC32_CD19, Hashtag4 for VC33_CD19, Hashtag5 for VC30_Basal, Hashtag6 for VC31_Basal, Hashtag7 for VC32_Basal, Hashtag8 for VC33_Basal
CART_RNA_6


title: CART_RNA_VC13_VC14_DC15_VC17_Duplicate1

description:
Hashtag1 for VC13_CD19,  Hashtag3 for VC15_CD19, Hashtag4 for VC17_CD19, Hashtag5 for VC13_Basal, Hashtag6 for VC14_Basal, Hashtag7 for VC15_Basal, Hashtag8 for VC17_Basal
CART_RNA_W


title: Uterus, Knockout, 3


title: CART_RNA_VC09_VC10_DC11_VC12_Duplicate2

description:
Hashtag1 for VC09_CD19, Hashtag2 for VC10_CD19, Hashtag3 for VC11_CD19, Hashtag4 for VC12_CD19, Hashtag5 for VC09_Basal, Hashtag6 for VC10_Basal, Hashtag7 for VC11_Basal, Hashtag8 for VC12_Basal
CART_RNA_V


title: CART_RNA_VC09_VC10_DC11_VC12_Duplicate1

description:
Hashtag1 for VC09_CD19, Hashtag2 for VC10_CD19, Hashtag3 for VC11_CD19, Hashtag4 for VC12_CD19, Hashtag5 for VC09_Basal, Hashtag6 for VC10_Basal, Hashtag7 for VC11_Basal, Hashtag8 for VC12_Basal
CART_RNA_U


title: Uterus, Knockout, 1


title: CART_RNA_VC26_VC27_DC28_VC29_Duplicate2

description:
Hashtag1 for VC26_CD19, Hashtag2 for VC27_CD19, Hashtag3 for VC28_CD19, Hashtag4 for VC29_CD19, Hashtag5 for VC26_Basal, Hashtag6 for VC27_Basal, Hashtag7 for VC28_Basal, Hashtag8 for VC29_Basal
CART_RNA_4


title: Liver_bulk_Adar1wt/wt_rep3

source_name: Liver

value: Liver

value: Ifih1-/- Adar1wt/wt Alb-Cre+

tag: Sex

value: female

value: 7 weeks


title: CART_RNA_VC05_VC06_DC07_VC08_Duplicate2

description:
Hashtag1 for VC05_CD19, Hashtag2 for VC06_CD19, Hashtag3 for VC07_CD19, Hashtag4 for VC08_CD19, Hashtag5 for VC05_Basal, Hashtag6 for VC06_Basal, Hashtag7 for VC07_Basal, Hashtag8 for VC08_Basal
CART_RNA_T


title: CART_RNA_VC26_VC27_DC28_VC29_Duplicate1

description:
Hashtag1 for VC26_CD19, Hashtag2 for VC27_CD19, Hashtag3 for VC28_CD19, Hashtag4 for VC29_CD19, Hashtag5 for VC26_Basal, Hashtag6 for VC27_Basal, Hashtag7 for VC28_Basal, Hashtag8 for VC29_Basal
CART_RNA_3


title: cDC1_KO_2

data_processing:
Raw reads were then aligned to mouse genome GRCm38 using Kallisto and removed adaptor sequences. Lowly expressed genes were excluded if total number of reads was lower than 10. Differential gene expression analysis was performed using the DESeq2 and Gene Ontology made by using the package ClusterProfiler v4.1.0. Differentially expressed genes were considered when FDR<0.05
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file contains raw reads for all the samples.

extract_protocol:
spleens were isolated and digested for 15 and 30 minutes respectively, in the presence of Liberase (50µg/ml, Sigma-Aldrich) and DNAse (250µg/ml, Sigma-Aldrich) in PBS supplemented with 5% FCS (Sigma-aldrich). Organs were then mashed through a 70µm filter and spleens were treated with ACK lysis buffer(BioLegend) for red blood cell elimination. Prepared cell suspensions were then stained with FACS antibodies: cDC1 (Lin-CD11c+MHCII+CD64-XCR1+CD11b-), cDC2 (Lin-CD11c+MHCII+CD64-XCR1-CD11b+) and pDCs (Lin-CD64-CD11cintCD11b-BST2+). Cells were stained and FACS sorted into 500uL of Trizol LS and RNA was then isolated using Qiagen miRNeasy isolation kit following the manufacturer’s instructions.
RNA libraries were prepared using the SMARTER mRNA-seq library prep kit protocol.

value: Spleen

value: conventional Dendritic Cell 1

value: HDAC1 Mx1-Cre

value: Mice were treated with PolyI/C to induce gene recombination, and cells sorted 2 weeks after.


title: CART_RNA_DC61_DC65_DC66_DC67_Duplicate2

description:
Hashtag1 for DC61_CD19, Hashtag2 for DC65_CD19, Hashtag3 for DC66_CD19, Hashtag4 for DC67_CD19, Hashtag5 for DC61_Basal, Hashtag6 for DC65_Basal, Hashtag7 for DC66_Basal, Hashtag8 for DC67_Basal
CART_RNA_16

value: PBMCs

value: Manufactured CAR T cells

value: GEX


title: pDC KO_1

value: plasmacytoid Dendritic Cell


title: Uterus, Control, 3


title: CART_RNA_VC22_VC23_DC24_VC25_Duplicate2

description:
Hashtag1 for VC22_CD19, Hashtag2 for VC23_CD19, Hashtag3 for VC24_CD19, Hashtag4 for VC25_CD19, Hashtag5 for VC22_Basal, Hashtag6 for VC23_Basal, Hashtag7 for VC24_Basal, Hashtag8 for VC25_Basal
CART_RNA_2


title: cDC1_KO_3


title: cDC1_KO_1


title: Uterus, Control, 2


title: cDC2_WT_3

value: conventional Dendritic Cell 2

value: HDAC1 floxed


title: CART_RNA_VC01_VC03_DC04_VC16_Duplicate1

description:
Hashtag1 for VC01_CD19, Hashtag2 for VC03_CD19, Hashtag3 for VC04_CD19, Hashtag4 for VC16_CD19, Hashtag5 for VC01_Basal, Hashtag6 for VC03_Basal, Hashtag7 for VC04_Basal, Hashtag8 for VC16_Basal
CART_RNA_Q


title: pDC_WT_3


title: cDC2_KO_3


title: Uterus, Control, 1

value: Pregnant uterus

value: 7.5 days post coitus


title: CART_RNA_VC18_VC19_DC20_VC21_Duplicate2

description:
Hashtag1 for VC18_CD19, Hashtag2 for VC19_CD19, Hashtag3 for VC20_CD19, Hashtag4 for VC21_CD19, Hashtag5 for VC18_Basal, Hashtag6 for VC19_Basal, Hashtag7 for VC20_Basal, Hashtag8 for VC21_Basal
CART_RNA_Z


title: cDC1_WT_3


title: cDC2 KO_2


title: CART_RNA_DC43_DC45_DC76_DC79_Duplicate1

description:
Hashtag1 for DC43_CD19, Hashtag2 for DC45_CD19, Hashtag3 for DC76_CD19, Hashtag4 for DC79_CD19, Hashtag5 for DC43_Basal, Hashtag6 for DC45_Basal, Hashtag7 for DC76_Basal, Hashtag8 for DC79_Basal
CART_RNA_M


title: cDC1_WT_2


title: CART_RNA_DC46_DC55_DC69_DC70_Duplicate1

description:
Hashtag1 for DC46_CD19, Hashtag2 for DC55_CD19, Hashtag3 for DC69_CD19, Hashtag4 for DC70_CD19, Hashtag5 for DC46_Basal, Hashtag6 for DC55_Basal, Hashtag7 for DC69_Basal, Hashtag8 for DC70_Basal
CART_RNA_K


title: cDC2 WT_2


title: pDC KO_3


title: pDC WT_1


title: CART_RNA_VC01_VC03_DC04_VC16_Duplicate2

description:
Hashtag1 for VC01_CD19, Hashtag2 for VC03_CD19, Hashtag3 for VC04_CD19, Hashtag4 for VC16_CD19, Hashtag5 for VC01_Basal, Hashtag6 for VC03_Basal, Hashtag7 for VC04_Basal, Hashtag8 for VC16_Basal
CART_RNA_R


title: CART_RNA_VC05_VC06_DC07_VC08_Duplicate1

description:
Hashtag1 for VC05_CD19, Hashtag2 for VC06_CD19, Hashtag3 for VC07_CD19, Hashtag4 for VC08_CD19, Hashtag5 for VC05_Basal, Hashtag6 for VC06_Basal, Hashtag7 for VC07_Basal, Hashtag8 for VC08_Basal
CART_RNA_S


title: pDC KO_2


title: cDC2 KO_1


title: CART_RNA_DC51_DC68_DC80_VC02_Duplicate2

description:
Hashtag1 for DC51_CD19, Hashtag2 for DC68_CD19, Hashtag3 for DC80_CD19, Hashtag4 for VC02_CD19, Hashtag5 for DC51_Basal, Hashtag6 for DC68_Basal, Hashtag7 for DC80_Basal, Hashtag8 for VC02_Basal
CART_RNA_P


title: CART_RNA_DC50_DC62_DC64_DC73_Duplicate2

description:
Hashtag1 for DC50_CD19, Hashtag2 for DC62_CD19, Hashtag3 for DC64_CD19, Hashtag4 for DC73_CD19, Hashtag5 for DC50_Basal, Hashtag6 for DC62_Basal, Hashtag7 for DC64_Basal, Hashtag8 for DC73_Basal
CART_RNA_H


title: CART_RNA_DC51_DC68_DC80_VC02_Duplicate1

description:
Hashtag1 for DC51_CD19, Hashtag2 for DC68_CD19, Hashtag3 for DC80_CD19, Hashtag4 for VC02_CD19, Hashtag5 for DC51_Basal, Hashtag6 for DC68_Basal, Hashtag7 for DC80_Basal, Hashtag8 for VC02_Basal
CART_RNA_O


title: cDC2-WT2-H3K27Ac

data_processing:
CUT&Run fastq files were trimmed using TrimGalore and aligned to mouse genome (mm10) using Bowtie2 (--local, --very-sensitive, --no-mixed, --no-discordant, --dovetail). SAMtools was used to fix mates of paired end reads, remove PCR duplicates of IgG sample, merge, sort and index bam files, while a CUT&Run-specific blacklist was removed from the bam files using BEDtools .
Assembly: mm10
Supplementary files format and content: .bed files contain peak information; .bw files allow visualization into IGV.

extract_protocol:
5*10^5 HDAC1-deficient cDC2 were FACS sorted from 3 pooled animals per replicate and genotype (2 replicates per genotype). Prior to FACS sorting, spleens were prepared as mentioned above and were depleted of dead cells/debris and cDC1 by using debris removal and XCR1 microbeads (Miltenyi). Eluted fractions were then enriched with CD11c microbeads resulting in cDC2 population with >80% purity. cDC2s were then FACS sorted to obtain >99% pure cDC2 population (BST2-CD11c+MHCII+XCR1-CD11b+SIRPA+) which was immediately utilized for sample preparation. For CUT and Run, cells were washed once in Buffer 1 (1x eBioscience Permeabilization buffer, 1x EDTA-free Protease Inhibitor cocktail, 0.5mM Spermidine) for 3 minutes at 600 x g and incubated on ice for 1 hour with a 1:200 dilution of H3K27ac antibody (Cell Signaling: 8173S) or rabbit IgG (Cell Signaling; #2729S) in a V-shaped 96-well plate. Next, cells were washed twice with Buffer 1, resuspended in 700 ng/mL pAG/Mnase and incubated on ice for 1 hour. After three washes in Buffer 2 (0.02% digitonin, 0.5mM Spermidine, 1x EDTA-free Protease Inhibitor cocktail in DPBS), pAG/Mnase was activated with 2mM CaCl2for 1 hour on ice. The reaction was quenched with 100µl 2x Stop buffer (Buffer 2 supplemented with 20mM EDTA and4mM EGTA) and incubated for 10 minutes at 37°C. Cells were then spun at 17,000 x g for 5 min and the supernatant was transferred to a fresh tube. DNA was isolated with NEB Monarch PCR and DNA clean up. Libraries were prepared using 1ng using NEBNext® Ultra™ II DNA Library Prep Kit, cleaned up using 1 volume of SPRI beads and subjected to PE150 sequencing.
DNA was isolated with NEB Monarch PCR and DNA clean up. Libraries were prepared using 1ng using NEBNext® Ultra™ II DNA Library Prep Kit, cleaned up using 1 volume of SPRI beads and subjected to PE150 sequencing.

value: Mice were treated with PolyI/C to induce gene recombination, and cells sorted 2 weeks after. 3 (2 Females 1 Male) independent mice were pooled into one single sample before FACS sorting for each biological replicate.


title: CART_RNA_DC47_DC72_DC74_DC81_Duplicate2

description:
Hashtag1 for DC47_CD19, Hashtag2 for DC72_CD19, Hashtag3 for DC74_CD19, Hashtag4 for DC81_CD19, Hashtag5 for DC47_Basal, Hashtag6 for DC72_Basal, Hashtag7 for DC74_Basal, Hashtag8 for DC81_Basal
CART_RNA_F


title: cDC2-WT1-IgG


title: CART_RNA_DC43_DC45_DC76_DC79_Duplicate2

description:
Hashtag1 for DC43_CD19, Hashtag2 for DC45_CD19, Hashtag3 for DC76_CD19, Hashtag4 for DC79_CD19, Hashtag5 for DC43_Basal, Hashtag6 for DC45_Basal, Hashtag7 for DC76_Basal, Hashtag8 for DC79_Basal
CART_RNA_N


title: pDC WT_2


title: cDC2 WT_1


title: CART_RNA_DC42_DC44_DC63_DC82_Duplicate1

description:
Hashtag1 for DC42_CD19, Hashtag2 for DC44_CD19, Hashtag3 for DC63_CD19, Hashtag4 for DC82_CD19, Hashtag5 for DC42_Basal, Hashtag6 for DC44_Basal, Hashtag7 for DC63_Basal, Hashtag8 for DC82_Basal
CART_RNA_I


title: CART_RNA_DC48_DC52_DC71_DC78_Duplicate1

description:
Hashtag1 for DC48_CD19, Hashtag2 for DC52_CD19, Hashtag3 for DC71_CD19, Hashtag4 for DC78_CD19, Hashtag5 for DC48_Basal, Hashtag6 for DC52_Basal, Hashtag7 for DC71_Basal, Hashtag8 for DC78_Basal
CART_RNA_C


title: CART_RNA_DC50_DC62_DC64_DC73_Duplicate1

description:
Hashtag1 for DC50_CD19, Hashtag2 for DC62_CD19, Hashtag3 for DC64_CD19, Hashtag4 for DC73_CD19, Hashtag5 for DC50_Basal, Hashtag6 for DC62_Basal, Hashtag7 for DC64_Basal, Hashtag8 for DC73_Basal
CART_RNA_G


title: CART_RNA_DC47_DC72_DC74_DC81_Duplicate1

description:
Hashtag1 for DC47_CD19, Hashtag2 for DC72_CD19, Hashtag3 for DC74_CD19, Hashtag4 for DC81_CD19, Hashtag5 for DC47_Basal, Hashtag6 for DC72_Basal, Hashtag7 for DC74_Basal, Hashtag8 for DC81_Basal
CART_RNA_E


title: cDC1_WT_1


title: CART_RNA_ND585_ND463_ND502_ND317_Duplicate1

description:
Hashtag1 for ND585_CD19, Hashtag2 for ND463_CD19, Hashtag3 for ND502_CD19, Hashtag4 for ND317_CD19, Hashtag5 for ND585_Basal, Hashtag6 for ND463_Basal, Hashtag7 for ND502_Basal, Hashtag8 for ND317_Basal
CART_RNA_A


title: CART_RNA_DC48_DC52_DC71_DC78_Duplicate2

description:
Hashtag1 for DC48_CD19, Hashtag2 for DC52_CD19, Hashtag3 for DC71_CD19, Hashtag4 for DC78_CD19, Hashtag5 for DC48_Basal, Hashtag6 for DC52_Basal, Hashtag7 for DC71_Basal, Hashtag8 for DC78_Basal
CART_RNA_D


title: cDC2-KO1-IgG


title: cDC2-WT1-H3k27Ac


title: cDC2-KO2-IgG


title: CART_RNA_DC42_DC44_DC63_DC82_Duplicate2

description:
Hashtag1 for DC42_CD19, Hashtag2 for DC44_CD19, Hashtag3 for DC63_CD19, Hashtag4 for DC82_CD19, Hashtag5 for DC42_Basal, Hashtag6 for DC44_Basal, Hashtag7 for DC63_Basal, Hashtag8 for DC82_Basal
CART_RNA_J


title: cDC2-WT2-IgG


title: CART_RNA_DC46_DC55_DC69_DC70_Duplicate2

description:
Hashtag1 for DC46_CD19, Hashtag2 for DC55_CD19, Hashtag3 for DC69_CD19, Hashtag4 for DC70_CD19, Hashtag5 for DC46_Basal, Hashtag6 for DC55_Basal, Hashtag7 for DC69_Basal, Hashtag8 for DC70_Basal
CART_RNA_L


title: CART_RNA_ND585_ND463_ND502_ND317_Duplicate2

description:
Hashtag1 for ND585_CD19, Hashtag2 for ND463_CD19, Hashtag3 for ND502_CD19, Hashtag4 for ND317_CD19, Hashtag5 for ND585_Basal, Hashtag6 for ND463_Basal, Hashtag7 for ND502_Basal, Hashtag8 for ND317_Basal
CART_RNA_B


title: 48_C16_WT_2

city: Bethesda

first: Teruhiko

last: Yoshida

address: 10 Center Drive, 9N208

department: NIDDK - KDB

institute: National Institutes of Health

data_processing:
Illumina RTA v3.4.4 software was used fro base calling, Bcl2fastq v2.17 was used for sample demultiplexing
Adapters from the samples were trimmed using Cutadapt 1.18 software
Genome mapping and transcript annotation were using STAR v2.7.0f with reference genome mm10.
The gene expression quantification analysis was performed for all samples using RSEM 1.3.1
Assembly: mm10
Supplementary files format and content: xlsx file contains rawcount matrix from RSEM

source_name: Mouse Kidney Cortex

extract_protocol:
Mice were euthanized and collected kidneys in their week of 12 weeks of age. Mouse kidney outer cortex tissues were dissected and homogenized in QIAzol. Total RNA samples were extracted by RNeasy Plus Universal Kit (QIAGEN, Hilden, Germany) following manufacture’s protocol including removal of genomic DNA step.
RNA libraries were prepared for sequencing using standard Illumina TruSeq Stranded mRNA library protocol.

treatment_protocol: C16 treatment group mice received 10µg/kg body weight of C16 in 10ml/kg body weight 0.5%DMSO-PBS intraperitoneally three times a week from 6 weeks to 12 weeks of age.

value: Kidney Cortex

value: WT


title: cDC2-KO2-H3K27Ac


title: 46_Ctrl_Tg_3

value: Control


title: cDC2-KO1-H3K27ac


title: 52_C16_Tg_3


title: 51_C16_Tg_2


title: 50_C16_Tg_1


title: 49_C16_WT_3


title: 45_Ctrl_Tg_2


title: 47_C16_WT_1


title: Enl-T1, TDI-11055, scRNA-seq

city: Philadelphia

first: Liling

last: Wan

state: PA

address: 421 Curie Blvd

department: Cancer Biology

institute: University of Pennsylvania

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were performed using CellRanger software (v6.1.2).
Assembly: mm10
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: kidney

extract_protocol:
Kidneys from E15.5 Enl-WT, Enl-T1, and Enl-T1 with TDI-11055 treatment embryos were harvested and incubated with digestion solution containing Enzyme P, Enzyme D, and Enzyme A from the Multi Tissue Dissociation Kit 2 (Miltenyi Biotec, #130-110-203) in a gentleMACS C tube. The tissues were digested on the gentleMACS Octo Dissociator with Heaters run program 37C_Multi_E. The samples were resuspended and filtered through 70 µm strainer, followed by one wash with 15 ml PBS. After centrifugation at 300×g for 10 min, the cell pellet was incubated with 10 volumes of 1X Red blood cell lysis solution (Miltenyi Biotec, #130-094-183) for 2 min at RT. Then, the samples were centrifuged at 300×g for 5 min at RT and resuspended with PBS for further steps. Cell number and viability were measured on a Countess AutoCounter (Invitrogen, #C10227).
scRNA-seq was performed with Chromium Next GEM Single Cell 3’ Reagent Kit V3.1 (10x Genomics, #PN-1000269) in accordance with the manufacturer’s instructions (10x Genomics, CG000388 RevB). Briefly, 10,000 live cells were loaded by targeting 6,000 cell recovery. The GEM was generated on Chromium Next GEM Chip G in the Chromium Controller. After the GEM-RT incubation and cleanup, cDNA was amplified and cleaned up. Agilent Bioanalyzer High Sensitivity DNA kit (Agilent, #5067-4626) was used for post-cDNA quality control and quantification. Next, the library was constructed according to the manufacturer’s manual. Qubit was used for DNA concentration measurement and Agilent Bioanalyzer High Sensitivity DNA kit was used for library quality control according to the manufacturer’s manual.

treatment_protocol: we treated pregnant mice with vehicle or TDI-11055 (100 mg/kg q.d.) via oral injection from E10.5, a time point when nephrogenesis starts during mouse kidney development, to E14.5, followed by collection of kidneys on E15.5.

value: kidney


title: Enl-T1, no treatment, scRNA-seq

description: 10x Genomics


title: HEK293 cells, ENL-T2, TDI-11055, replicate 2

data_processing:
RNA-seq samples were sequenced using Illumina NextSeq 550.
Raw reads were mapped to the mouse reference genome (hg19) and transcriptome using HISAT2 v 2.2.1 with default parameters.
The raw counts for gene were calculated by featureCounts v2.0.2.
Differentially expressed genes between conditions were statistically determined using R package DESeq2 v1.40.1.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include gene raw count number for each sample

extract_protocol:
RNeasy UCP Micro kit (Qiagen, #73934) was used to extract total RNA and remove genomic DNA.
500ng total RNA was used for library preparation using polyA mRNA magnetic Isolation module (NEB, #E7490) and RNA library prep kit (NEB, #7770) following manufacturer’s instructions. The library quality was assessed on an Agilent Bioanalyzer DNA chip (Agilent, #5067-1504).

treatment_protocol: Cells were treated with DMSO or TDI-11055 (10 μM) for 24 hrs


title: HEK293 cells, ENL-T2, TDI-11055, replicate 1


title: Enl-WT, no treatment, scRNA-seq

description: 10x Genomics


title: Enl-T1, snATAC-seq

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were performed using CellRanger-ATAC software (v2.1.0).
Assembly: mm10
Supplementary files format and content: Tab-seperated values files and matrix files

extract_protocol:
Kidneys from E15.5 Enl-WT, Enl-T1, and Enl-T1 with TDI-11055 treatment embryos were harvested and incubated with digestion solution containing Enzyme P, Enzyme D, and Enzyme A from the Multi Tissue Dissociation Kit 2 (Miltenyi Biotec, #130-110-203) in a gentleMACS C tube. The tissues were digested on the gentleMACS Octo Dissociator with Heaters run program 37C_Multi_E. The samples were resuspended and filtered through 70 µm strainer, followed by one wash with 15 ml PBS. After centrifugation at 300×g for 10 min, the cell pellet was incubated with 10 volumes of 1X Red blood cell lysis solution (Miltenyi Biotec, #130-094-183) for 2 min at RT. Then, the samples were centrifuged at 300×g for 5 min at RT and resuspended with PBS for further steps. Cell number and viability were measured on a Countess AutoCounter (Invitrogen, #C10227).
snATAC-seq was performed with Chromium Next GEM Single Cell ATAC Reagent Kit V2 (10x Genomics, #PN-1000406) in accordance with the manufacturer’s instructions (10x Genomics, CG000496 RevA). Briefly, 10,000 nuclei were loaded and incubated in the transposition buffer by targeting 6,000 nuclei recovery. The GEM was generated on Chromium Next GEM Chip H in the Chromium Controller. After the GEM incubation cleanup, the library was constructed according to the manufacturer’s manual. Qubit was used for DNA concentration measurement and Agilent Bioanalyzer High Sensitivity DNA kit was used for library quality control according to the manufacturer’s manual.


title: 43_Ctrl_WT_3


title: 42_Ctrl_WT_2


title: HEK293 cells, ENL-T2, DMSO, replicate 2

value: DMSO


title: HEK293 cells, ENL-T2, DMSO, replicate 1


title: 41_Ctrl_WT_1


title: HEK293 cells, ENL-T2, TDI-11055, replicate 3


title: 44_Ctrl_Tg_1


title: Enl-WT, snATAC-seq

description: 10x Genomics


title: HEK293 cells, ENL-T2, DMSO, replicate 3


title: HEK293 cells, ENL-T1, DMSO, replicate 3


title: E14tg2a, Dppa2_CtbpTKO_RRBS

city: Sanda

first: Yoshiyuki

last: Seki

state: hyogo

address: 1, Gakuen Uegahara

department: School of Biological and Environmental Sciences

country: Japan

institute: Kwansei Gakuin University

data_processing:
(RNA-seq) Sequence reads were trimmed using trimgalore (R-package) with option (-q 20 -j 4)
(RNA-seq) Trimed fasq files were aligned by Hisat2 to mm10 genome with defaults setting.
(RNA-seq) Read counts were extracted using R package FeatureCounts using mm10 KnownGenes.
(RRBS) Sequence reads were trimmed using trimgalore (R-package) with option (--rrbs --non_directional --paired --length 15)
(RRBS) Trimed fasq files were aligned using bismark with option (-- pbat)
(RRBS) CpG methylation was extracted using bismark_methylation_extractor
Assembly: mm10
Supplementary files format and content: tab-delimited files (RNA-seq)
Supplementary files format and content: BedGraph (RRBS)

growth_protocol: E14tg2a cells were maintained in GMEM with 10%FBS and LIF

extract_protocol:
Total RNAs were extracted using a PureLinkTM RNA Mini Kit (Ambion, Inc.)  Genomic DNAs were evtracted using Wizard® SV Genomic DNA Purification System 602 (Promega).
RNA-seq libraries were contructed using CollibriTM Stranded RNA library prep for ilIuminaTM Systems 582 (ThermoFisher Scientific). RRBS libraries were constructed using Premium RRBS kit V2.

value: Embryonic stem cells


title: HEK293 cells, ENL-T1, TDI-11055, replicate 2


title: HEK293 cells, ENL-T1, TDI-11055, replicate 3


title: HEK293 cells, ENL-T1, DMSO, replicate 1


title: Multiome rgc:ntr 24h ablation ascl1a KO day 7 RNA

first: Kevin

last: Emmerich

address: 1800 Orleans St

department: Ophthalmology

data_processing:
scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline (v4.3.0.1) and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs, and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly, the top 2,000 variable genes were identified and used to identify principal components (PCs) of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes (DEGs) were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster (minimum log2 foldchange cutoff of 0.25).
scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC-seq reads was performed using MACS2 in the ArchR package (v1.0.2). ATAC seq data was then processed using the pbmc scATAC-seq workflow with the Signac (v1.10.0) and Seurat (v4.3.0.1) packages for quality control, normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next, the ChromVar package (v1.18.0) was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells.
Assembly: GRCz11
Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes, features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files

molecule: nuclear RNA

organism: Danio rerio

source_name: Eye

extract_protocol:
scRNAseq: 40-60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain (10 eyes per 1 ml) (Worthington), and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin (Sigma-Aldrich) and 10 U/ml DNaseI (Roche). Cells were filtered through a 70-μm filter (Miltenyi Biotec), kept on ice until 10X genomics processing. scMultiomeseq: 40-60 eyes were dissected and flash-frozen in dry ice for ~15min before being transferred to a -80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression (GEX) protocol (CGOOO338). Briefly, frozen retinal tissues were lysed in ice-cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged, washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of ~3000-5000 nuclei/ml and kept on ice until 10x genomics processing.
Library preparation was then performed according to 10x genomics protocols.

value: Eye

tag: transgenic line

value: mtz, ascl1a gRNAs


title: E14tg2a, CtbpDKO_RRBS

value: CtbpDKO


title: Multiome rgc:ntr 24h ablation ascl1a KO day 7 ATAC

description:
JM_M_A
Ref genome Danio_rerio.GRCz11.108.chr.gtf.gz

library_source: genomic single cell


title: E14tg2a, WT_RRBS


title: E14tg2a, Dppa2KO_RRBS


title: HEK293 cells, ENL-WT, TDI-11055, replicate 3


title: HEK293 cells, ENL-WT, TDI-11055, replicate 2


title: HEK293 cells, ENL-T1, DMSO, replicate 2


title: E14tg2a, P7KO_rep2

description:
P7KO_rep2
WT_DuxKO_P7KO_P7OE.counts.txt


title: HEK293 cells, ENL-WT, DMSO, replicate 3


title: Multiome rgc:ntr 24h ablation wildtype day 7 RNA

value: mtz


title: Multiome rgc:ntr 24h ablation wildtype day 7 ATAC

description:
JM_C_A
Ref genome Danio_rerio.GRCz11.108.chr.gtf.gz


title: E14tg2a, P7KO_rep1

description:
P7KO_rep1
WT_DuxKO_P7KO_P7OE.counts.txt


title: HEK293 cells, ENL-T1, TDI-11055, replicate 1


title: E14tg2a, WT_rep5

description:
WT_rep5
WT_DuxKO_P7KO_P7OE.counts.txt


title: Multiome rgc:ntr preablation wildtype control day 5 ATAC

value: no mtz


title: HEK293 cells, Flag-ENL-T1, TDI-11055, ChIP-seq

data_processing:
ChIP-seq and CUT&Tag samples were sequenced using Illumina NextSeq 550.
Raw reads were mapped to the mouse reference genome (hg19) and transcriptome using Bowtie2 v 2.2.5 with default parameters.
Aligned BAM files were sorted using function samtools v 1.6. Secondary alignments, unmapped reads, and duplicate reads in the sorted bam files were filtered out using samtools v 1.6. The filtered and sorted bam files were then indexed using function indexBam from samtools v 1.6.
Peaks were called using MACS v 2.2.8, peaks were called at q ≤ 1E−10.
Filtered, sorted, indexed BAM files were converted to bigwig files using bamCoverage from deeptools v 3.5.2
Assembly: hg19
Supplementary files format and content: bigWig files are in an indexed binary format

extract_protocol:
Lysates were clarified from nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq sample libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit (NEB, #E7645L) following the manufacturer's instructions.  After adapter ligation, DNA was PCR amplified with Illumina primers for indicated cycles and the DNA size distribution was quantified on an Agilent Bioanalyzer DNA chip ( Agilent, #5067-1504).


title: E14tg2a, DuxKO_P7OE_rep2

description:
DuxKO_P7OE_rep2
WT_DuxKO_P7KO_P7OE.counts.txt


title: Multiome rgc:ntr preablation wildtype control day 5 RNA


title: Multiome rgc:ntr preablation ascl1a KO day 5 RNA

value: no mtz, ascl1a gRNAs


title: LNCaPHA-K205R-3-micro

city: Shanghai

first: Renjie

last: Cai

address: 280 Mohe Road, Baoshan District

department: Department of Oncology

institute: Shanghai 9th People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China

data_processing:
Unique raw fastq reads were mapped to the human transcriptome using STAR
STAR parameters:twopassMode Basic|--outSAMstrandField intronMotif|--alignSJstitchMismatchNmax 5 -1 5 5
RSEQC was used for comparison and statistics
Assembly: The transcripts in the sample are assembled by using stringtie software based on the location information file of the known transcripts on the genome
Supplementary files format and content: merged xls files include RPKM values for each Sample

source_name: LNCaP

growth_protocol: LNCaP cells were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted from the LNCaP stable cell lines using TRIzol (Invitrogen, CA, USA).
The total RNA was extracted using the VAHTS Universal V6 RNA seq Library Prep Kit ( Vazyme, NR604-02, Nanjing, China）for Illumina to construct the cDNA library.

value: LNCaP

value: Prostate cancer cells

value: KHSRP knockdown-reapplied HA-KHSRP-WT


title: E14tg2a, DuxKO_P7OE_rep1

description:
DuxKO_P7OE_rep1
WT_DuxKO_P7KO_P7OE.counts.txt


title: HEK293 cells, ENL-WT, DMSO, replicate 1


title: HEK293 cells, ENL-WT, TDI-11055, replicate 1


title: HEK293 cells, Input, DMSO, ChIP-seq


title: E14tg2a, WT_rep6

description:
WT_rep6
WT_DuxKO_P7KO_P7OE.counts.txt


title: Multiome rgc:ntr preablation ascl1a KO day 5 ATAC

value: nomtz, ascl1a gRNAs


title: E14tg2a, P7OE_rep1

description:
P7OE_rep1
WT_DuxKO_P7KO_P7OE.counts.txt


title: HEK293 cells, Flag-ENL-T1, DMSO, ChIP-seq


title: E14tg2a, P7OE_rep2

description:
P7OE_rep2
WT_DuxKO_P7KO_P7OE.counts.txt


title: Ablated rgc:ntr day 9 72h mtz

description:
TH136
Barcode start 12_72, end with -4
RGC_12+72h_features.tsv.gz
RGC_12+72h_matrix.mtx.gz
RGC_12+72h_barcodes.tsv.gz


title: LNCaPHA-K205R-2-micro


title: Ablated rgc:ntr day 6 12h mtz

description:
TH135
Barcode start 12_72, end with -3
RGC_12+72h_features.tsv.gz
RGC_12+72h_matrix.mtx.gz
RGC_12+72h_barcodes.tsv.gz


title: HEK293 cells, ENL-WT, DMSO, replicate 2


title: HEK293 cells, Flag-ENL-WT, DMSO, ChIP-seq


title: LNCaPVECTOR-3-micro


title: Unablated rgc:ntr day 6

description:
TH133
Barcode start 12_72, end with -1
RGC_12+72h_features.tsv.gz
RGC_12+72h_matrix.mtx.gz
RGC_12+72h_barcodes.tsv.gz


title: E14tg2a, DuxKO_rep3

description:
DuxKO_rep3
WT_DuxKO_P7KO_P7OE.counts.txt

value: DuxKO


title: E14tg2a, DuxKO_rep4

description:
DuxKO_rep4
WT_DuxKO_P7KO_P7OE.counts.txt


title: LNCaPVECTOR-2-micro


title: Unablated rgc:ntr day 9

description:
TH134
Barcode start 12_72, end with -2
RGC_12+72h_features.tsv.gz
RGC_12+72h_matrix.mtx.gz
RGC_12+72h_barcodes.tsv.gz


title: Pgb1.1A.12h.3

city: Winnipeg

first: Claudio

last: Stasolla

state: MB

address: 66 Dafoe Road

department: Plant Science

country: Canada

institute: University of Manitoba

data_processing:
Raw RNA-seq reads were aligned using HISAT2 (Kim et al., 2019).
Gene counts were quantified using featureCounts (Liao et al., 2014).
Assembly: Zea mays B73 RefGen_v4 (Zm-B73-GRAMENE-REFERENCE-4.0) genome assembly (Jiao et al., 2017), downloaded from the Maize Genetics and Genomics Database (MaizeGDB) (https://www.maizegdb.org).
Supplementary files format and content: Gene counts file containing raw counts (from featureCounts) of all genes for each sample

organism: Zea mays

source_name: QC of root tip

extract_protocol:
Quiescent centers (QCs) were gently separated from the weak wall junction with the proximal tissue after surgical removal of the root cap. RNA extraction from QC was carried out using the Ambion® RNaqueous® 152 micro kit.
Total RNA was submitted to Génome Québec (Montreal, Quebec) for library construction and sequencing, using NEBNext Multiplex Oligos for Illumina.

treatment_protocol: Roots of 5-day-old maize seedlings were submerged in a liquid solution [1/2 Murashige and Skoog (MS) medium] supplied with air (normoxic conditions) or 4% (v/v) oxygen/96% nitrogen (hypoxic conditions). Seedlings were collected at 6, 12, and 24 h during treatments.

value: QC of root tip

tag: timepoint

value: hypoxic


title: Ablated rgc:ntr day 7 24h mtz

description:
TH111
Barcode start 24_48, end with -2
RGC_24+48h_features.tsv.gz
RGC_24+48h_matrix.mtx.gz
RGC_24+48h_barcodes.tsv.gz


title: E14tg2a, WT_rep4

description:
WT_rep4
WT_DuxKO_P7KO_P7OE.counts.txt

tag: cell type

value: WT


title: LNCaPVECTOR-1-micro

tag: cell line


title: Pgb1.1A.12h.2

tag: treatment


title: E14tg2a, WT_rep3

description:
WT_rep3
WT_DuxKO_P7KO_P7OE.counts.txt


title: HEK293 cells, Flag-ENL-WT, TDI-11055, ChIP-seq


title: LNCaPsh-UTR-3-micro

value: KHSRP knockdown


title: Ablated rgc:ntr day 8 48h mtz

description:
TH104
Barcode start 24_48, end with -4
RGC_24+48h_features.tsv.gz
RGC_24+48h_matrix.mtx.gz
RGC_24+48h_barcodes.tsv.gz


title: Pgb1.1A.0h.3

value: normoxic